log started: Sun Nov 1 20:04:54 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 {A5 C3}
Sequence: A5
Sequence: C3
Joining A5 - C3
>
> check m
Checking 'm'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Warning: Close contact of 1.140193 angstroms between .R<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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: Sun Nov 1 20:05:47 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: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
total atoms in file: 63
>
> 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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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: 11.937 18.719 9.385
Total bounding box for atom centers: 34.719 34.719 34.719
(box expansion for 'iso' is 70.0%)
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 2 y= 2 z= 2
Adding box at: x=0 y=0 z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0 y=0 z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0 y=1 z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0 y=1 z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1 y=0 z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1 y=0 z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1 y=1 z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1 y=1 z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
Volume: 53253.502 A^3
Total mass 22154.600 amu, Density 0.691 g/cc
Added 1198 residues.
> quit
Quit
log started: Sun Nov 1 20:05:48 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: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
total atoms in file: 63
>
> 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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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: 11.937 18.719 9.385
Total bounding box for atom centers: 32.719 32.719 32.719
(box expansion for 'iso' is 76.5%)
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 2 y= 2 z= 2
Adding box at: x=0 y=0 z=0
Center of solvent box is: 9.387175, 9.387175, 9.387175
Adding box at: x=0 y=0 z=1
Center of solvent box is: 9.387175, 9.387175, -9.387175
Adding box at: x=0 y=1 z=0
Center of solvent box is: 9.387175, -9.387175, 9.387175
Adding box at: x=0 y=1 z=1
Center of solvent box is: 9.387175, -9.387175, -9.387175
Adding box at: x=1 y=0 z=0
Center of solvent box is: -9.387175, 9.387175, 9.387175
Adding box at: x=1 y=0 z=1
Center of solvent box is: -9.387175, 9.387175, -9.387175
Adding box at: x=1 y=1 z=0
Center of solvent box is: -9.387175, -9.387175, 9.387175
Adding box at: x=1 y=1 z=1
Center of solvent box is: -9.387175, -9.387175, -9.387175
Volume: 46190.939 A^3
Total mass 18137.032 amu, Density 0.652 g/cc
Added 975 residues.
> quit
Quit
log started: Sun Nov 1 20:05:48 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: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
total atoms in file: 63
>
> 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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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: 11.937 18.719 9.385
Total bounding box for atom centers: 33.719 33.719 33.719
(box expansion for 'iso' is 73.1%)
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: 49828.855 A^3
Total mass 19992.680 amu, Density 0.666 g/cc
Added 1078 residues.
> quit
Quit
log started: Sun Nov 1 20:05:48 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: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
total atoms in file: 63
>
> 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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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: 11.937 18.719 9.385
Total bounding box for atom centers: 33.919 33.919 33.919
(box expansion for 'iso' is 72.4%)
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: 50033.472 A^3
Total mass 20353.000 amu, Density 0.675 g/cc
Added 1098 residues.
> quit
Quit
log started: Sun Nov 1 20:05:48 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: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
total atoms in file: 63
>
> 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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 2
Unit is OK.
>
> solvatebox m TIP3PBOX 7.55 iso
Solute vdw bounding box: 11.937 18.719 9.385
Total bounding box for atom centers: 33.819 33.819 33.819
(box expansion for 'iso' is 72.8%)
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 20208.872 amu, Density 0.673 g/cc
Added 1090 residues.
> quit
Quit
log started: Sun Nov 1 20:05:49 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: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
total atoms in file: 63
>
> 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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 2
Unit is OK.
>
> solvateoct m TIP3PBOX 7.55 iso
Scaling up box by a factor of 1.259037 to meet diagonal cut criterion
Solute vdw bounding box: 11.937 18.719 9.385
Total bounding box for atom centers: 37.731 37.731 37.731
(box expansion for 'iso' is 62.0%)
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: 29049.594 A^3 (oct)
Total mass 14227.560 amu, Density 0.813 g/cc
Added 758 residues.
> remove m m.1092
remove: Argument #2 is type String must be of type: [molecule residue atom]
usage: remove <unit/residue/atom> <unit/residue/atom>
> remove m m.1091
remove: Argument #2 is type String must be of type: [molecule residue atom]
usage: remove <unit/residue/atom> <unit/residue/atom>
> remove m m.1090
remove: Argument #2 is type String must be of type: [molecule residue atom]
usage: remove <unit/residue/atom> <unit/residue/atom>
> remove m m.1089
remove: Argument #2 is type String must be of type: [molecule residue atom]
usage: remove <unit/residue/atom> <unit/residue/atom>
>
> 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: -13.88 -11.82 -12.92 13.29 12.59 15.21
sized: 18.12 20.18 19.08
edge: 32.00
Resolution: 1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 19.17% of box, grid points 6283
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (-3.30, -3.23, -3.07).
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: -18.10 -16.04 -17.14 17.51 16.81 19.43
sized: 45.90 47.96 46.86
edge: 64.00
Resolution: 1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume = 4.96% of box, grid points 13003
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (1.53, 5.70, 12.09).
(Replacing solvent molecule)
Placed Cl- in m at (-2.29, 6.97, 16.23).
(Replacing solvent molecule)
Placed Na+ in m at (-6.31, 6.14, 16.94).
(Replacing solvent molecule)
Placed Cl- in m at (2.66, -1.41, 18.62).
(Replacing solvent molecule)
Placed Na+ in m at (-2.38, -1.90, 17.33).
(Replacing solvent molecule)
Placed Cl- in m at (-6.75, 0.83, 17.30).
(Replacing solvent molecule)
Placed Na+ in m at (-2.15, 3.76, 16.27).
(Replacing solvent molecule)
Placed Cl- in m at (-0.09, 2.08, 16.96).
(Replacing solvent molecule)
Placed Na+ in m at (4.03, 0.94, 16.56).
(Replacing solvent molecule)
Placed Cl- in m at (5.55, 4.80, 13.73).
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.
** Warning: No sp2 improper torsion term for N*-CB-CB-NC
atoms are: N9 C5 C4 N3
** Warning: No sp2 improper torsion term for NB-CA-CB-CB
atoms are: N7 C6 C5 C4
total 11 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 747
)
(no restraints)
> quit
Quit
log started: Sun Nov 1 20:05:49 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: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
total atoms in file: 63
>
> 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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 2
Unit is OK.
>
> solvatebox m TIP3PBOX 7.55 iso
Solute vdw bounding box: 11.937 18.719 9.385
Total bounding box for atom centers: 33.819 33.819 33.819
(box expansion for 'iso' is 72.8%)
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 20208.872 amu, Density 0.673 g/cc
Added 1090 residues.
> remove m m.1092
> 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: -12.14 -15.69 -10.85 12.16 15.41 10.50
sized: 19.86 16.31 21.15
edge: 32.00
Resolution: 1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 19.22% of box, grid points 6297
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: -16.36 -19.91 -15.07 16.38 19.63 16.99
sized: 47.64 44.09 48.93
edge: 64.00
Resolution: 1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume = 5.00% of box, grid points 13117
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (6.29, 11.70, -6.64).
(Replacing solvent molecule)
Placed Cl- in m at (6.76, 7.42, -9.08).
(Replacing solvent molecule)
Placed Na+ in m at (5.36, 7.21, -12.35).
(Replacing solvent molecule)
Placed Cl- in m at (4.88, 12.09, -10.93).
(Replacing solvent molecule)
Placed Na+ in m at (1.98, 13.61, -11.25).
(Replacing solvent molecule)
Placed Cl- in m at (0.74, 11.91, -7.66).
(Replacing solvent molecule)
Placed Na+ in m at (-3.18, 11.42, -8.77).
(Replacing solvent molecule)
Placed Cl- in m at (-4.21, 3.57, -11.94).
(Replacing solvent molecule)
Placed Na+ in m at (-6.53, 3.90, -8.22).
(Replacing solvent molecule)
Placed Cl- in m at (-7.00, 8.44, -7.63).
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.
** Warning: No sp2 improper torsion term for N*-CB-CB-NC
atoms are: N9 C5 C4 N3
** Warning: No sp2 improper torsion term for NB-CA-CB-CB
atoms are: N7 C6 C5 C4
total 11 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: Sun Nov 1 20:05:49 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: A5, Terminal/beginning, was not found in name map.)
(Residue 1: C3, Terminal/last, was not found in name map.)
Joining A5 - C3
total atoms in file: 63
>
> 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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
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<A5 1>.A<H3' 26> and .R<C3 2>.A<H5' 6>
Checking parameters for unit 'm'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 2
Unit is OK.
>
> solvatebox m TIP3PBOX 7.55 iso
Solute vdw bounding box: 11.937 18.719 9.385
Total bounding box for atom centers: 33.819 33.819 33.819
(box expansion for 'iso' is 72.8%)
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 20208.872 amu, Density 0.673 g/cc
Added 1090 residues.
> remove m m.1092
> 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: -12.14 -15.69 -10.85 12.16 15.41 10.50
sized: 19.86 16.31 21.15
edge: 32.00
Resolution: 1.00 Angstrom.
Tree depth: 5
grid build: 0 sec
Volume = 19.22% of box, grid points 6297
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: -16.36 -19.91 -15.07 16.38 19.63 16.99
sized: 47.64 44.09 48.93
edge: 64.00
Resolution: 1.00 Angstrom.
Tree depth: 6
grid build: 0 sec
Volume = 5.00% of box, grid points 13117
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 0 sec
(Replacing solvent molecule)
Placed Na+ in m at (6.29, 11.70, -6.64).
(Replacing solvent molecule)
Placed Cl- in m at (6.76, 7.42, -9.08).
(Replacing solvent molecule)
Placed Na+ in m at (5.36, 7.21, -12.35).
(Replacing solvent molecule)
Placed Cl- in m at (4.88, 12.09, -10.93).
(Replacing solvent molecule)
Placed Na+ in m at (1.98, 13.61, -11.25).
(Replacing solvent molecule)
Placed Cl- in m at (0.74, 11.91, -7.66).
(Replacing solvent molecule)
Placed Na+ in m at (-3.18, 11.42, -8.77).
(Replacing solvent molecule)
Placed Cl- in m at (-4.21, 3.57, -11.94).
(Replacing solvent molecule)
Placed Na+ in m at (-6.53, 3.90, -8.22).
(Replacing solvent molecule)
Placed Cl- in m at (-7.00, 8.44, -7.63).
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.
** Warning: No sp2 improper torsion term for N*-CB-CB-NC
atoms are: N9 C5 C4 N3
** Warning: No sp2 improper torsion term for NB-CA-CB-CB
atoms are: N7 C6 C5 C4
total 11 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