log started: Tue May 3 11:18:51 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 8 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:52 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 9 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:52 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 10 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:52 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 11 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:53 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 12 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:53 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 13 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:53 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 14 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:54 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 15 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:54 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 16 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:54 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 17 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:55 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 18 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:55 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 19 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:55 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 20 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:55 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 21 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:56 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 22 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:56 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 23 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:56 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 24 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:57 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 25 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:57 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 26 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:57 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 27 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:57 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 28 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:58 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 29 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:58 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 30 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:58 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 31 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 32 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 33 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 34 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:18:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 35 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:00 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 36 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:00 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 37 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:00 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 38 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:00 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 39 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:01 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 40 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:01 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 41 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:01 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 42 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 43 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 44 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 45 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 46 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 47 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 48 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 49 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 50 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:04 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 51 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:04 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 52 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:04 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 53 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:04 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 54 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:04 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 55 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:05 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 56 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:05 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 57 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:05 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 58 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:05 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 59 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 60 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 61 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 62 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 63 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 64 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 65 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 66 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 67 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 68 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 69 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 70 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 71 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 72 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 73 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 74 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 75 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 76 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 77 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 78 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 79 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 80 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 81 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 82 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 83 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 84 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:12 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 85 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:12 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 86 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:12 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 87 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:12 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 88 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:13 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 89 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:13 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 90 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:13 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 91 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:14 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 92 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:14 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 93 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:14 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 94 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:15 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 95 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:15 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 96 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:15 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 97 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 98 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 99 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 100 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 101 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:17 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 102 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:17 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 103 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:17 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 104 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:18 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 105 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:18 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 106 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:18 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 107 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:18 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 108 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:19 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 109 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:19 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 110 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:19 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 111 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 112 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 113 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 114 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 115 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:21 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 116 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:21 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 117 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:21 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 118 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 119 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 120 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 121 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:23 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 122 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:23 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 123 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:23 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 124 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:23 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 125 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:24 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 126 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:24 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 127 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:24 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 128 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:24 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 129 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:25 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 130 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:25 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 131 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:25 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 132 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:25 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 133 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:26 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 134 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:26 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 135 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:26 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 136 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:26 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 137 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 138 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 139 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 140 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 141 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 142 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:28 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 143 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:28 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 144 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:28 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 145 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:28 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 146 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:28 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 147 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:29 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 148 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:29 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 149 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:29 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 150 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:29 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 151 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:29 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 152 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:30 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 153 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:30 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 154 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:30 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 155 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:31 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 156 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:31 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 157 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:31 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 158 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:32 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 159 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:32 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 160 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:32 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 161 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:33 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 162 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:33 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 163 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:33 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 164 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:33 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 165 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:34 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 166 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:34 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 167 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:34 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 168 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:35 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 169 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:35 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 170 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:35 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 171 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:36 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 172 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:36 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 173 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:36 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 174 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:36 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 175 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:37 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 176 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:37 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 177 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:37 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 178 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:38 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 179 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:38 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 180 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:38 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 181 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:38 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 182 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:39 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 183 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:39 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 184 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:39 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 185 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:40 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 186 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:40 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 187 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:40 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 188 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:41 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 189 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:41 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 190 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:41 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 191 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:42 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 192 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:42 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 193 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:42 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 194 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:42 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 195 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:43 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 196 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:43 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 197 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:43 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 198 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:44 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 199 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:44 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 200 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:44 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 201 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:45 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 202 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:45 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 203 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:45 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 204 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:45 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 205 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:46 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 206 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:46 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 207 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:46 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 208 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:46 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 209 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:47 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 210 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:47 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 211 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:47 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 212 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:47 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 213 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:48 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 214 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:48 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 215 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:48 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 216 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:48 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 217 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:49 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 218 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:49 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 219 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:49 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 220 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:49 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 221 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:50 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 222 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:50 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 223 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:50 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 224 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:50 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 225 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:51 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 226 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:51 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 227 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:51 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 228 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:51 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 229 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:51 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 230 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:52 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 231 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:52 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 232 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:52 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 233 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:52 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 234 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:53 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 235 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:53 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 236 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:53 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 237 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:53 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 238 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:54 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 239 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:54 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 240 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:54 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 241 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:54 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 242 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:55 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 243 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:55 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 244 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:55 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 245 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:55 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 246 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:56 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 247 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:56 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 248 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:56 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 249 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:57 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 250 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:57 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 251 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:57 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 252 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:57 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 253 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:58 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 254 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:58 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 255 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:58 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 256 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:58 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 257 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 258 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 259 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 260 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 261 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:19:59 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 262 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:00 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 263 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:00 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 264 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:00 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 265 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:00 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 266 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:01 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 267 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:01 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 268 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:01 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 269 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:01 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 270 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:01 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 271 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 272 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 273 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 274 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 275 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:02 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 276 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 277 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 278 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 279 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 280 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:03 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 281 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:04 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 282 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:04 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 283 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:04 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 284 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:05 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 285 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:05 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 286 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:05 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 287 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:05 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 288 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 289 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 290 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 291 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:06 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 292 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 293 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 294 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 295 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 296 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 297 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 298 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 299 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 300 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 301 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 302 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 303 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 304 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 305 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 306 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 307 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 308 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 309 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 310 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 311 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 312 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 313 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 314 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:11 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 315 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:13 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 316 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:13 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 317 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:13 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 318 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:14 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 319 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:14 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 320 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:14 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 321 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:15 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 322 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:15 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 323 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:15 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 324 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:15 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 325 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 326 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 327 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 328 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 329 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:17 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 330 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:17 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 331 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:17 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 332 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:17 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 333 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:18 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 334 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:18 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 335 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:18 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 336 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:18 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 337 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:19 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 338 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:19 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 339 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:19 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 340 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:19 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 341 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 342 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 343 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 344 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 345 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:20 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 346 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:21 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 347 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:21 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 348 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:21 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 349 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:21 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 350 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:21 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 351 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 352 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 353 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 354 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 355 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 356 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:22 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 357 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:23 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 358 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:23 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 359 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:23 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 360 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:23 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 361 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:24 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 362 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:24 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 363 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:24 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 364 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:25 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 365 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:25 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 366 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:25 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 367 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:25 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 368 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:26 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 369 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:26 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 370 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:26 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 371 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:26 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 372 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 373 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 374 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Could not open file init.pdb: not found > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > > > check m check: Argument #1 is type String must be of type: [unit molecule residue atom] usage: check [parmset] > > solvatebox m TIP3PBOX 375 iso solvateBox: Argument #1 is type String must be of type: [unit] usage: solvateBox [iso] [closeness] > quit Quit log started: Tue May 3 11:20:27 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib log started: Tue May 3 11:22:07 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Loading PDB file: ./init.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: U5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining U5 - C3 total atoms in file: 60 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > solvatebox m TIP3PBOX 8 iso Solute vdw bounding box: 12.757 11.053 9.462 Total bounding box for atom centers: 28.757 28.757 28.757 (box expansion for 'iso' is 20.1%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Volume: 31866.708 A^3 Total mass 12384.896 amu, Density 0.645 g/cc Added 657 residues. > quit Quit log started: Tue May 3 11:22:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Loading PDB file: ./init.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: U5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining U5 - C3 total atoms in file: 60 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > solvatebox m TIP3PBOX 9 iso Solute vdw bounding box: 12.757 11.053 9.462 Total bounding box for atom centers: 30.757 30.757 30.757 (box expansion for 'iso' is 18.6%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Volume: 39273.221 A^3 Total mass 15159.360 amu, Density 0.641 g/cc Added 811 residues. > quit Quit log started: Tue May 3 11:22:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Loading PDB file: ./init.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: U5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining U5 - C3 total atoms in file: 60 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > solvatebox m TIP3PBOX 10 iso Solute vdw bounding box: 12.757 11.053 9.462 Total bounding box for atom centers: 32.757 32.757 32.757 (box expansion for 'iso' is 17.3%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Volume: 46190.939 A^3 Total mass 18204.064 amu, Density 0.654 g/cc Added 980 residues. > quit Quit log started: Tue May 3 11:22:08 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Loading PDB file: ./init.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: U5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining U5 - C3 total atoms in file: 60 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > solvatebox m TIP3PBOX 11 iso Solute vdw bounding box: 12.757 11.053 9.462 Total bounding box for atom centers: 34.757 34.757 34.757 (box expansion for 'iso' is 16.2%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Volume: 53253.502 A^3 Total mass 22221.632 amu, Density 0.693 g/cc Added 1203 residues. > quit Quit log started: Tue May 3 11:22:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Loading PDB file: ./init.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: U5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining U5 - C3 total atoms in file: 60 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > solvatebox m TIP3PBOX 10.5 iso Solute vdw bounding box: 12.757 11.053 9.462 Total bounding box for atom centers: 33.757 33.757 33.757 (box expansion for 'iso' is 16.7%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Volume: 49828.855 A^3 Total mass 20167.808 amu, Density 0.672 g/cc Added 1089 residues. > quit Quit log started: Tue May 3 11:22:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Loading PDB file: ./init.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: U5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining U5 - C3 total atoms in file: 60 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > solvateoct m TIP3PBOX 10.5 iso Scaling up box by a factor of 1.266609 to meet diagonal cut criterion Solute vdw bounding box: 12.757 11.053 9.462 Total bounding box for atom centers: 39.356 39.356 39.356 (box expansion for 'iso' is 14.1%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 3 y= 3 z= 3 Adding box at: x=0 y=0 z=0 Center of solvent box is: 18.774349, 18.774349, 18.774349 Adding box at: x=0 y=0 z=1 Center of solvent box is: 18.774349, 18.774349, 0.000000 Adding box at: x=0 y=0 z=2 Center of solvent box is: 18.774349, 18.774349, -18.774349 Adding box at: x=0 y=1 z=0 Center of solvent box is: 18.774349, 0.000000, 18.774349 Adding box at: x=0 y=1 z=1 Center of solvent box is: 18.774349, 0.000000, 0.000000 Adding box at: x=0 y=1 z=2 Center of solvent box is: 18.774349, 0.000000, -18.774349 Adding box at: x=0 y=2 z=0 Center of solvent box is: 18.774349, -18.774349, 18.774349 Adding box at: x=0 y=2 z=1 Center of solvent box is: 18.774349, -18.774349, 0.000000 Adding box at: x=0 y=2 z=2 Center of solvent box is: 18.774349, -18.774349, -18.774349 Adding box at: x=1 y=0 z=0 Center of solvent box is: 0.000000, 18.774349, 18.774349 Adding box at: x=1 y=0 z=1 Center of solvent box is: 0.000000, 18.774349, 0.000000 Adding box at: x=1 y=0 z=2 Center of solvent box is: 0.000000, 18.774349, -18.774349 Adding box at: x=1 y=1 z=0 Center of solvent box is: 0.000000, 0.000000, 18.774349 Adding box at: x=1 y=1 z=1 Center of solvent box is: 0.000000, 0.000000, 0.000000 Adding box at: x=1 y=1 z=2 Center of solvent box is: 0.000000, 0.000000, -18.774349 Adding box at: x=1 y=2 z=0 Center of solvent box is: 0.000000, -18.774349, 18.774349 Adding box at: x=1 y=2 z=1 Center of solvent box is: 0.000000, -18.774349, 0.000000 Adding box at: x=1 y=2 z=2 Center of solvent box is: 0.000000, -18.774349, -18.774349 Adding box at: x=2 y=0 z=0 Center of solvent box is: -18.774349, 18.774349, 18.774349 Adding box at: x=2 y=0 z=1 Center of solvent box is: -18.774349, 18.774349, 0.000000 Adding box at: x=2 y=0 z=2 Center of solvent box is: -18.774349, 18.774349, -18.774349 Adding box at: x=2 y=1 z=0 Center of solvent box is: -18.774349, 0.000000, 18.774349 Adding box at: x=2 y=1 z=1 Center of solvent box is: -18.774349, 0.000000, 0.000000 Adding box at: x=2 y=1 z=2 Center of solvent box is: -18.774349, 0.000000, -18.774349 Adding box at: x=2 y=2 z=0 Center of solvent box is: -18.774349, -18.774349, 18.774349 Adding box at: x=2 y=2 z=1 Center of solvent box is: -18.774349, -18.774349, 0.000000 Adding box at: x=2 y=2 z=2 Center of solvent box is: -18.774349, -18.774349, -18.774349 Volume: 32862.230 A^3 (oct) Total mass 16474.528 amu, Density 0.832 g/cc Added 884 residues. > remove m m.1091 remove: Argument #2 is type String must be of type: [molecule residue atom] usage: remove > remove m m.1090 remove: Argument #2 is type String must be of type: [molecule residue atom] usage: remove > remove m m.1089 remove: Argument #2 is type String must be of type: [molecule residue atom] usage: remove > > addions m Na+ 0 1 Na+ ion required to neutralize. Adding 1 counter ions to "m" using 1A grid Total solute charge: -1.00 Max atom radius: 2.10 Grid extends from solute vdw + 1.37 to 7.47 Box: enclosing: -11.27 -12.20 -12.36 11.99 11.97 10.89 sized: 20.73 19.80 19.64 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 15.83% of box, grid points 5188 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-0.84, 9.13, 2.61). Done adding ions. > addions m Na+ 5 Cl- 5 Na+ has a charge of 0. Adding the ions anyway. Adding 10 counter ions to "m" using 1A grid Total solute charge: 0.00 Max atom radius: 2.10 Grid extends from solute vdw + 5.59 to 11.69 Box: enclosing: -15.49 -16.42 -16.58 16.21 20.82 15.11 sized: 48.51 47.58 47.42 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.58% of box, grid points 11999 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (4.67, -9.05, -5.96). (Replacing solvent molecule) Placed Cl- in m at (7.19, -11.11, -6.96). (Replacing solvent molecule) Placed Na+ in m at (10.34, -9.92, -4.55). (Replacing solvent molecule) Placed Cl- in m at (8.59, -7.11, -4.99). (Replacing solvent molecule) Placed Na+ in m at (8.48, -8.10, -8.78). (Replacing solvent molecule) Placed Cl- in m at (4.04, -6.68, -10.43). (Replacing solvent molecule) Placed Na+ in m at (0.13, -5.77, -12.18). (Replacing solvent molecule) Placed Cl- in m at (-1.88, -6.86, -14.30). (Replacing solvent molecule) Placed Na+ in m at (-6.41, -3.62, -14.86). (Replacing solvent molecule) Placed Cl- in m at (-8.21, -2.88, -9.96). Done adding ions. > > saveamberparm m full.topo non-randomized.crds Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 12 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 873 ) (no restraints) > quit Quit log started: Tue May 3 11:22:09 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Loading PDB file: ./init.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: U5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining U5 - C3 total atoms in file: 60 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > solvatebox m TIP3PBOX 10.5 iso Solute vdw bounding box: 12.757 11.053 9.462 Total bounding box for atom centers: 33.757 33.757 33.757 (box expansion for 'iso' is 16.7%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Volume: 49828.855 A^3 Total mass 20167.808 amu, Density 0.672 g/cc Added 1089 residues. > remove m m.1091 > remove m m.1090 > remove m m.1089 > > addions m Na+ 0 1 Na+ ion required to neutralize. Adding 1 counter ions to "m" using 1A grid Total solute charge: -1.00 Max atom radius: 2.10 Grid extends from solute vdw + 1.37 to 7.47 Box: enclosing: -12.40 -11.11 -10.74 12.45 11.84 10.57 sized: 19.60 20.89 21.26 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 15.84% of box, grid points 5192 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (0.08, 5.59, -5.38). Done adding ions. > addions m Na+ 5 Cl- 5 Na+ has a charge of 0. Adding the ions anyway. Adding 10 counter ions to "m" using 1A grid Total solute charge: 0.00 Max atom radius: 2.10 Grid extends from solute vdw + 5.59 to 11.69 Box: enclosing: -16.62 -15.33 -17.07 16.67 17.28 14.79 sized: 47.38 48.67 46.93 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.42% of box, grid points 11582 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (0.87, -9.72, 1.39). (Replacing solvent molecule) Placed Cl- in m at (1.74, -12.00, -2.78). (Replacing solvent molecule) Placed Na+ in m at (1.94, -14.90, -6.78). (Replacing solvent molecule) Placed Cl- in m at (-1.17, -9.59, 5.47). (Replacing solvent molecule) Placed Na+ in m at (-1.47, -8.50, 12.00). (Replacing solvent molecule) Placed Cl- in m at (-3.13, -5.58, 13.58). (Replacing solvent molecule) Placed Na+ in m at (-6.13, -6.09, 8.49). (Replacing solvent molecule) Placed Cl- in m at (-9.35, -0.98, 10.94). (Replacing solvent molecule) Placed Na+ in m at (-3.82, -1.67, 13.63). (Replacing solvent molecule) Placed Cl- in m at (-7.00, -10.33, 11.14). Done adding ions. > > saveamberparm m full.topo non-randomized.crds Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 12 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 1075 ) (no restraints) > quit Quit log started: Tue May 3 11:22:10 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-lonepeak/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = loadpdb init.pdb Loading PDB file: ./init.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: U5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining U5 - C3 total atoms in file: 60 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.269303 angstroms between .R.A and .R.A Warning: Close contact of 1.414096 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. > > solvatebox m TIP3PBOX 10.5 iso Solute vdw bounding box: 12.757 11.053 9.462 Total bounding box for atom centers: 33.757 33.757 33.757 (box expansion for 'iso' is 16.7%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.387175, 9.387175, 9.387175 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.387175, 9.387175, -9.387175 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.387175, -9.387175, 9.387175 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.387175, -9.387175, -9.387175 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.387175, 9.387175, 9.387175 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.387175, 9.387175, -9.387175 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.387175, -9.387175, 9.387175 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.387175, -9.387175, -9.387175 Volume: 49828.855 A^3 Total mass 20167.808 amu, Density 0.672 g/cc Added 1089 residues. > remove m m.1091 > remove m m.1090 > remove m m.1089 > > addions m Na+ 0 1 Na+ ion required to neutralize. Adding 1 counter ions to "m" using 1A grid Total solute charge: -1.00 Max atom radius: 2.10 Grid extends from solute vdw + 1.37 to 7.47 Box: enclosing: -12.40 -11.11 -10.74 12.45 11.84 10.57 sized: 19.60 20.89 21.26 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 15.84% of box, grid points 5192 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (0.08, 5.59, -5.38). Done adding ions. > addions m Na+ 5 Cl- 5 Na+ has a charge of 0. Adding the ions anyway. Adding 10 counter ions to "m" using 1A grid Total solute charge: 0.00 Max atom radius: 2.10 Grid extends from solute vdw + 5.59 to 11.69 Box: enclosing: -16.62 -15.33 -17.07 16.67 17.28 14.79 sized: 47.38 48.67 46.93 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.42% of box, grid points 11582 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (0.87, -9.72, 1.39). (Replacing solvent molecule) Placed Cl- in m at (1.74, -12.00, -2.78). (Replacing solvent molecule) Placed Na+ in m at (1.94, -14.90, -6.78). (Replacing solvent molecule) Placed Cl- in m at (-1.17, -9.59, 5.47). (Replacing solvent molecule) Placed Na+ in m at (-1.47, -8.50, 12.00). (Replacing solvent molecule) Placed Cl- in m at (-3.13, -5.58, 13.58). (Replacing solvent molecule) Placed Na+ in m at (-6.13, -6.09, 8.49). (Replacing solvent molecule) Placed Cl- in m at (-9.35, -0.98, 10.94). (Replacing solvent molecule) Placed Na+ in m at (-3.82, -1.67, 13.63). (Replacing solvent molecule) Placed Cl- in m at (-7.00, -10.33, 11.14). Done adding ions. > > saveamberparm m full.topo non-randomized.crds Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 12 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 1075 ) (no restraints) > quit Quit