log started: Fri Nov 6 15:27:11 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.tip3p Could not open file frcmod.tip3p: not found > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > > m = sequence {C5 C3} Sequence: C5 Sequence: C3 Joining C5 - C3 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140192 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > savepdb m init.pdb Writing pdb file: init.pdb > > quit Quit log started: Fri Nov 6 15:27:22 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 8 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.802 33.802 33.802 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20202.858 amu, Density 0.673 g/cc Added 1091 residues. > quit Quit log started: Fri Nov 6 15:27:22 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvateoct m TIP3PBOX 8 iso Scaling up box by a factor of 1.294129 to meet diagonal cut criterion Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 38.508 38.508 38.508 (box expansion for 'iso' is 52.2%) 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: 30833.448 A^3 (oct) Total mass 15176.394 amu, Density 0.817 g/cc Added 812 residues. > remove m m.1093 remove: Argument #2 is type String must be of type: [molecule residue atom] usage: remove > remove m m.1092 remove: Argument #2 is type String must be of type: [molecule residue atom] usage: remove > 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 > > 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: -13.99 -10.42 -13.12 13.01 13.48 14.62 sized: 18.01 21.58 18.88 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 18.55% of box, grid points 6078 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-3.46, -2.50, -3.31). 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: -18.21 -14.64 -17.34 17.23 17.70 18.84 sized: 45.79 49.36 46.66 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.86% of box, grid points 12749 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (2.91, 6.71, 6.95). (Replacing solvent molecule) Placed Cl- in m at (5.53, 6.38, 7.42). (Replacing solvent molecule) Placed Na+ in m at (7.34, 5.54, 9.34). (Replacing solvent molecule) Placed Cl- in m at (8.96, 4.81, 6.89). (Replacing solvent molecule) Placed Na+ in m at (9.42, 6.25, 2.72). (Replacing solvent molecule) Placed Cl- in m at (11.08, 6.50, -1.02). (Replacing solvent molecule) Placed Na+ in m at (12.62, 2.21, 4.50). (Replacing solvent molecule) Placed Cl- in m at (7.90, 3.15, 1.24). (Replacing solvent molecule) Placed Na+ in m at (12.79, 2.84, -3.63). (Replacing solvent molecule) Placed Cl- in m at (14.20, 1.09, 1.85). 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 801 ) (no restraints) > quit Quit log started: Fri Nov 6 15:27:23 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 8 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.802 33.802 33.802 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20202.858 amu, Density 0.673 g/cc Added 1091 residues. > remove m m.1093 > remove m m.1092 > remove m m.1091 > remove m m.1090 > > 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: -12.08 -15.00 -10.80 12.21 15.08 10.42 sized: 19.92 17.00 21.20 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 18.47% of box, grid points 6053 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-1.05, -0.51, 5.30). 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: -16.30 -19.22 -15.02 16.43 19.30 16.99 sized: 47.70 44.78 48.98 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.88% of box, grid points 12805 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (6.31, 8.22, -5.16). (Replacing solvent molecule) Placed Cl- in m at (9.39, 7.70, -5.36). (Replacing solvent molecule) Placed Na+ in m at (13.40, 9.52, -5.04). (Replacing solvent molecule) Placed Cl- in m at (13.96, 11.28, -2.97). (Replacing solvent molecule) Placed Na+ in m at (14.43, 8.62, -0.96). (Replacing solvent molecule) Placed Cl- in m at (15.43, 3.56, -0.89). (Replacing solvent molecule) Placed Na+ in m at (12.15, 2.05, -2.52). (Replacing solvent molecule) Placed Cl- in m at (11.19, 5.85, 7.05). (Replacing solvent molecule) Placed Na+ in m at (14.10, 4.27, 1.77). (Replacing solvent molecule) Placed Cl- in m at (12.64, 5.12, -2.12). 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 1076 ) (no restraints) > quit Quit log started: Fri Nov 6 15:27:23 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 8 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.802 33.802 33.802 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20202.858 amu, Density 0.673 g/cc Added 1091 residues. > remove m m.1093 > remove m m.1092 > remove m m.1091 > remove m m.1090 > > 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: -12.08 -15.00 -10.80 12.21 15.08 10.42 sized: 19.92 17.00 21.20 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 18.47% of box, grid points 6053 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-1.05, -0.51, 5.30). 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: -16.30 -19.22 -15.02 16.43 19.30 16.99 sized: 47.70 44.78 48.98 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.88% of box, grid points 12805 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (6.31, 8.22, -5.16). (Replacing solvent molecule) Placed Cl- in m at (9.39, 7.70, -5.36). (Replacing solvent molecule) Placed Na+ in m at (13.40, 9.52, -5.04). (Replacing solvent molecule) Placed Cl- in m at (13.96, 11.28, -2.97). (Replacing solvent molecule) Placed Na+ in m at (14.43, 8.62, -0.96). (Replacing solvent molecule) Placed Cl- in m at (15.43, 3.56, -0.89). (Replacing solvent molecule) Placed Na+ in m at (12.15, 2.05, -2.52). (Replacing solvent molecule) Placed Cl- in m at (11.19, 5.85, 7.05). (Replacing solvent molecule) Placed Na+ in m at (14.10, 4.27, 1.77). (Replacing solvent molecule) Placed Cl- in m at (12.64, 5.12, -2.12). 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 1076 ) (no restraints) > quit Quit log started: Fri Nov 6 15:28:19 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 8 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.802 33.802 33.802 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20202.858 amu, Density 0.673 g/cc Added 1091 residues. > quit Quit log started: Fri Nov 6 15:28:20 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 31.802 31.802 31.802 (box expansion for 'iso' is 68.4%) 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: 41568.017 A^3 Total mass 16275.370 amu, Density 0.650 g/cc Added 873 residues. > quit Quit log started: Fri Nov 6 15:28:20 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.5 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 32.802 32.802 32.802 (box expansion for 'iso' is 65.4%) 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: 46243.223 A^3 Total mass 18311.178 amu, Density 0.658 g/cc Added 986 residues. > quit Quit log started: Fri Nov 6 15:28:20 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.6 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.002 33.002 33.002 (box expansion for 'iso' is 64.8%) 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: 46990.706 A^3 Total mass 18491.338 amu, Density 0.653 g/cc Added 996 residues. > quit Quit log started: Fri Nov 6 15:28:20 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.7 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.202 33.202 33.202 (box expansion for 'iso' is 64.2%) 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: 47483.242 A^3 Total mass 18707.530 amu, Density 0.654 g/cc Added 1008 residues. > quit Quit log started: Fri Nov 6 15:28:20 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.8 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.402 33.402 33.402 (box expansion for 'iso' is 63.7%) 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: 47727.965 A^3 Total mass 19211.978 amu, Density 0.668 g/cc Added 1036 residues. > quit Quit log started: Fri Nov 6 15:28:21 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.9 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.602 33.602 33.602 (box expansion for 'iso' is 63.1%) 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: 48794.245 A^3 Total mass 19590.314 amu, Density 0.667 g/cc Added 1057 residues. > quit Quit log started: Fri Nov 6 15:28:21 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 8 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.802 33.802 33.802 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20202.858 amu, Density 0.673 g/cc Added 1091 residues. > quit Quit log started: Fri Nov 6 15:28:21 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.95 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.702 33.702 33.702 (box expansion for 'iso' is 62.9%) 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 19842.538 amu, Density 0.661 g/cc Added 1071 residues. > quit Quit log started: Fri Nov 6 15:28:21 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.96 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.722 33.722 33.722 (box expansion for 'iso' is 62.8%) 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 19986.666 amu, Density 0.666 g/cc Added 1079 residues. > quit Quit log started: Fri Nov 6 15:28:21 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.97 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.742 33.742 33.742 (box expansion for 'iso' is 62.8%) 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 20094.762 amu, Density 0.670 g/cc Added 1085 residues. > quit Quit log started: Fri Nov 6 15:28:22 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.98 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.762 33.762 33.762 (box expansion for 'iso' is 62.7%) 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 20094.762 amu, Density 0.670 g/cc Added 1085 residues. > quit Quit log started: Fri Nov 6 15:28:22 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.99 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.782 33.782 33.782 (box expansion for 'iso' is 62.7%) 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 20094.762 amu, Density 0.670 g/cc Added 1085 residues. > quit Quit log started: Fri Nov 6 15:28:22 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 8 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.802 33.802 33.802 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20202.858 amu, Density 0.673 g/cc Added 1091 residues. > quit Quit log started: Fri Nov 6 15:28:22 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.995 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.792 33.792 33.792 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20166.826 amu, Density 0.672 g/cc Added 1089 residues. > quit Quit log started: Fri Nov 6 15:28:22 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvateoct m TIP3PBOX 7.995 iso Scaling up box by a factor of 1.294154 to meet diagonal cut criterion Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 38.495 38.495 38.495 (box expansion for 'iso' is 52.2%) 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: 30804.083 A^3 (oct) Total mass 15122.346 amu, Density 0.815 g/cc Added 809 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: -13.85 -10.51 -12.96 13.15 13.39 14.79 sized: 18.15 21.49 19.04 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 18.55% of box, grid points 6078 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-3.32, -2.59, -3.15). 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: -18.07 -14.73 -17.18 17.37 17.61 19.01 sized: 45.93 49.27 46.82 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.86% of box, grid points 12749 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (3.04, 6.61, 7.11). (Replacing solvent molecule) Placed Cl- in m at (5.66, 6.28, 7.59). (Replacing solvent molecule) Placed Na+ in m at (7.47, 5.45, 9.50). (Replacing solvent molecule) Placed Cl- in m at (9.09, 4.71, 7.06). (Replacing solvent molecule) Placed Na+ in m at (9.55, 6.15, 2.88). (Replacing solvent molecule) Placed Cl- in m at (11.21, 6.40, -0.85). (Replacing solvent molecule) Placed Na+ in m at (12.76, 2.12, 4.67). (Replacing solvent molecule) Placed Cl- in m at (8.03, 3.06, 1.40). (Replacing solvent molecule) Placed Na+ in m at (12.92, 2.75, -3.47). (Replacing solvent molecule) Placed Cl- in m at (14.34, 1.00, 2.01). 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 798 ) (no restraints) > quit Quit log started: Fri Nov 6 15:28:22 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.995 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.792 33.792 33.792 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20166.826 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: -12.08 -15.00 -10.80 12.21 15.08 10.42 sized: 19.92 17.00 21.20 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 18.47% of box, grid points 6053 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-1.05, -0.51, 5.30). 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: -16.30 -19.22 -15.02 16.43 19.30 16.99 sized: 47.70 44.78 48.98 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.88% of box, grid points 12805 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (6.31, 8.22, -5.16). (Replacing solvent molecule) Placed Cl- in m at (9.39, 7.70, -5.36). (Replacing solvent molecule) Placed Na+ in m at (13.40, 9.52, -5.04). (Replacing solvent molecule) Placed Cl- in m at (13.96, 11.28, -2.97). (Replacing solvent molecule) Placed Na+ in m at (14.43, 8.62, -0.96). (Replacing solvent molecule) Placed Cl- in m at (15.43, 3.56, -0.89). (Replacing solvent molecule) Placed Na+ in m at (12.15, 2.05, -2.52). (Replacing solvent molecule) Placed Cl- in m at (11.19, 5.85, 7.05). (Replacing solvent molecule) Placed Na+ in m at (14.10, 4.27, 1.77). (Replacing solvent molecule) Placed Cl- in m at (12.64, 5.12, -2.12). 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: Fri Nov 6 15:28:23 2015 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff12SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadoff atomic_ions.lib Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force 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: C5, Terminal/beginning, was not found in name map.) (Residue 1: C3, Terminal/last, was not found in name map.) Joining C5 - C3 total atoms in file: 61 > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > > > check m Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.140355 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > > solvatebox m TIP3PBOX 7.995 iso Solute vdw bounding box: 11.855 17.802 9.225 Total bounding box for atom centers: 33.792 33.792 33.792 (box expansion for 'iso' is 62.6%) 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: 49828.855 A^3 Total mass 20166.826 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: -12.08 -15.00 -10.80 12.21 15.08 10.42 sized: 19.92 17.00 21.20 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 18.47% of box, grid points 6053 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (-1.05, -0.51, 5.30). 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: -16.30 -19.22 -15.02 16.43 19.30 16.99 sized: 47.70 44.78 48.98 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 4.88% of box, grid points 12805 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in m at (6.31, 8.22, -5.16). (Replacing solvent molecule) Placed Cl- in m at (9.39, 7.70, -5.36). (Replacing solvent molecule) Placed Na+ in m at (13.40, 9.52, -5.04). (Replacing solvent molecule) Placed Cl- in m at (13.96, 11.28, -2.97). (Replacing solvent molecule) Placed Na+ in m at (14.43, 8.62, -0.96). (Replacing solvent molecule) Placed Cl- in m at (15.43, 3.56, -0.89). (Replacing solvent molecule) Placed Na+ in m at (12.15, 2.05, -2.52). (Replacing solvent molecule) Placed Cl- in m at (11.19, 5.85, 7.05). (Replacing solvent molecule) Placed Na+ in m at (14.10, 4.27, 1.77). (Replacing solvent molecule) Placed Cl- in m at (12.64, 5.12, -2.12). 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: Mon Jan 25 12:01:43 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" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-kepler//dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-kepler//dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries, nucleic acids >> # >> loadOff amino12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-kepler//dat/leap/lib/amino12.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-kepler//dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-kepler//dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff nucleic12.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-kepler//dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN >> # >> # Load water and ions >> # >> loadOff atomic_ions.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-kepler//dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-kepler//dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and nucleic acids >> # (note: no NHYP! use neutral form for now) >> # >> addPdbResMap { >> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "G" "G5" } { 1 "G" "G3" } >> { 0 "A" "A5" } { 1 "A" "A3" } >> { 0 "C" "C5" } { 1 "C" "C3" } >> { 0 "U" "U5" } { 1 "U" "U3" } >> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >> # some old Amber residue names for RNA: >> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >> # some really old Amber residue names, assuming DNA: >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> # uncomment out the following if you have this old style RNA files: >> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >> # { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # try to be good about reading in really old atom names as well: >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "O2*" "O2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'" } >> { "H2*2" "H2''" } >> { "HO*2" "HO2'" } >> { "H2'1" "H2'" } >> { "H2'2" "H2''" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'" } >> { "H5*2" "H5''" } >> { "H5'1" "H5'" } >> { "H5'2" "H5''" } >> { "HO'2" "HO2'" } >> { "H5T" "HO5'" } >> { "H3T" "HO3'" } >> { "O1'" "O4'" } >> { "OA" "OP1" } >> { "OB" "OP2" } >> { "O1P" "OP1" } >> { "O2P" "OP2" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > > m = sequence {C5 C3} Sequence: C5 Sequence: C3 Joining C5 - C3 > > savemol2 m cc.mol2 saveMol2: Improper number of arguments! usage: saveMol2