log started: Mon Jun 4 17:19:08 2012 Log file: ./leap.log >>> # >>> # ----- leaprc for loading the ff10 force field >>> # ----- NOTE: this is designed for PDB format 3! >>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >>> # >>> # load atom type hybridizations >>> # >>> addAtomTypes { >>> { "H" "H" "sp3" } >>> { "HO" "H" "sp3" } >>> { "HS" "H" "sp3" } >>> { "H1" "H" "sp3" } >>> { "H2" "H" "sp3" } >>> { "H3" "H" "sp3" } >>> { "H4" "H" "sp3" } >>> { "H5" "H" "sp3" } >>> { "HW" "H" "sp3" } >>> { "HC" "H" "sp3" } >>> { "HA" "H" "sp3" } >>> { "HP" "H" "sp3" } >>> { "HZ" "H" "sp3" } >>> { "OH" "O" "sp3" } >>> { "OS" "O" "sp3" } >>> { "O" "O" "sp2" } >>> { "O2" "O" "sp2" } >>> { "OP" "O" "sp2" } >>> { "OW" "O" "sp3" } >>> { "CT" "C" "sp3" } >>> { "CX" "C" "sp3" } >>> { "CH" "C" "sp3" } >>> { "CS" "C" "sp2" } >>> { "C" "C" "sp2" } >>> { "C*" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CB" "C" "sp2" } >>> { "CC" "C" "sp2" } >>> { "CN" "C" "sp2" } >>> { "CM" "C" "sp2" } >>> { "CK" "C" "sp2" } >>> { "CQ" "C" "sp2" } >>> { "CD" "C" "sp2" } >>> { "C5" "C" "sp2" } >>> { "C4" "C" "sp2" } >>> { "CP" "C" "sp2" } >>> { "CI" "C" "sp3" } >>> { "CJ" "C" "sp2" } >>> { "CW" "C" "sp2" } >>> { "CV" "C" "sp2" } >>> { "CR" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CY" "C" "sp2" } >>> { "C0" "C" "sp2" } >>> { "MG" "Mg" "sp3" } >>> { "N" "N" "sp2" } >>> { "NA" "N" "sp2" } >>> { "N2" "N" "sp2" } >>> { "N*" "N" "sp2" } >>> { "NP" "N" "sp2" } >>> { "NQ" "N" "sp2" } >>> { "NB" "N" "sp2" } >>> { "NC" "N" "sp2" } >>> { "NT" "N" "sp3" } >>> { "NY" "N" "sp2" } >>> { "N3" "N" "sp3" } >>> { "S" "S" "sp3" } >>> { "SH" "S" "sp3" } >>> { "P" "P" "sp3" } >>> { "LP" "" "sp3" } >>> { "EP" "" "sp3" } >>> { "F" "F" "sp3" } >>> { "Cl" "Cl" "sp3" } >>> { "Br" "Br" "sp3" } >>> { "I" "I" "sp3" } >>> { "F-" "F" "sp3" } >>> { "Cl-" "Cl" "sp3" } >>> { "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" } >>> } addAtomTypes: type Cl- - max length is 2 addAtomTypes: type Br- - max length is 2 addAtomTypes: type Li+ - max length is 2 addAtomTypes: type Na+ - max length is 2 addAtomTypes: type Rb+ - max length is 2 addAtomTypes: type Cs+ - max length is 2 addAtomTypes: type Mg+ - max length is 2 >>> # >>> # Load the main parameter set. >>> # >>> parm10 = loadamberparams parm10.dat Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >>> # >>> # Load main chain and terminating amino acid libraries, nucleic acids >>> # >>> loadOff amino10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/amino10.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >>> loadOff aminoct10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminoct10.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >>> loadOff aminont10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminont10.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >>> loadOff nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/nucleic10.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: U Loading: U3 Loading: U5 Loading: UN >>> # >>> # Load water and ions >>> # >>> loadOff ions08.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >>> loadOff solvents.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >>> HOH = TP3 >>> WAT = TP3 >>> >>> # >>> # Define the PDB name map for the amino acids and nucleic acids >>> # >>> addPdbResMap { >>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >>> { 0 "G" "G5" } { 1 "G" "G3" } >>> { 0 "A" "A5" } { 1 "A" "A3" } >>> { 0 "C" "C5" } { 1 "C" "C3" } >>> { 0 "U" "U5" } { 1 "U" "U3" } >>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >>> # some old Amber residue names for RNA: >>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >>> # some really old Amber residue names, assuming DNA: >>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >>> # uncomment out the following if you have this old style RNA files: >>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >>> >>> } >>> >>> # try to be good about reading in really old atom names as well: >>> addPdbAtomMap { >>> { "O5*" "O5'" } >>> { "C5*" "C5'" } >>> { "C4*" "C4'" } >>> { "O4*" "O4'" } >>> { "C3*" "C3'" } >>> { "O3*" "O3'" } >>> { "C2*" "C2'" } >>> { "O2*" "O2'" } >>> { "C1*" "C1'" } >>> { "C5M" "C7" } >>> { "H1*" "H1'" } >>> { "H2*1" "H2'" } >>> { "H2*2" "H2''" } >>> { "H2'1" "H2'" } >>> { "H2'2" "H2''" } >>> { "H3*" "H3'" } >>> { "H4*" "H4'" } >>> { "H5*1" "H5'" } >>> { "H5*2" "H5''" } >>> { "H5'1" "H5'" } >>> { "H5'2" "H5''" } >>> { "HO'2" "HO2'" } >>> { "H5T" "HO5'" } >>> { "H3T" "HO3'" } >>> { "O1'" "O4'" } >>> { "OA" "OP1" } >>> { "OB" "OP2" } >>> { "O1P" "OP1" } >>> { "O2P" "OP2" } >>> } >>> >>> # >>> # assume that most often proteins use HIE >>> # >>> NHIS = NHIE >>> HIS = HIE >>> CHIS = CHIE >> >> >> # Extra constant pH libraries for Amino Acids >> loadOFF constph.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/constph.lib Loading: AS2 Loading: AS4 Loading: GL4 >> >> # Extra constant pH libraries for Nucleic Acids >> loadOFF all_prot_nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_prot_nucleic10.lib Loading: A3E Loading: A3P Loading: A5E Loading: A5P Loading: AE Loading: AP Loading: C3E Loading: C3P Loading: C5E Loading: C5P Loading: CE Loading: CP Loading: D3A Loading: D3AE Loading: D3C Loading: D3CE Loading: D3G Loading: D3GE Loading: D3T Loading: D3TE Loading: D5A Loading: D5AE Loading: D5C Loading: D5CE Loading: D5G Loading: D5GE Loading: D5T Loading: D5TE Loading: DAE Loading: DAP Loading: DCE Loading: DCP Loading: DGD Loading: DGE Loading: DTD Loading: DTE Loading: G3D Loading: G3E Loading: G5D Loading: G5E Loading: GD Loading: GE Loading: U3D Loading: U3E Loading: U5D Loading: U5E Loading: UD Loading: UE >> loadOFF cph_nucleic_caps.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/cph_nucleic_caps.lib Loading: CH3 Loading: MOC >> >> # Necessary constant pH force field modifications >> loadAmberParams frcmod.constph Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.constph Reading force field modification type file (frcmod) Reading title: Force field modifcations for titrations >> loadAmberParams frcmod.protonated_nucleic Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.protonated_nucleic Reading force field modification type file (frcmod) Reading title: Force field modifications for protonated nucleic acids (UNKNOWN ATOM TYPE: NX) (UNKNOWN ATOM TYPE: OX) (UNKNOWN ATOM TYPE: HD) >> >> # PBRadii must be mbondi2, corresponding to the proper reference energies >> set default PBRadii mbondi2 Using H(N)-modified Bondi radii > > > # Create blocked amino acid systems. > system = seq { ACE ASP NME } ERROR: syntax error saveamberparam system asp.prmtop asp.inpcrd ERROR: syntax error > help Help is available on the following subjects: _cmd_options_ _types_ add addAtomTypes addIons addIons2 addPath addPdbAtomMap addPdbResMap alias alignAxes bond bondByDistance center charge check clearPdbAtomMap clearPdbResMap clearVariables combine copy createAtom createParmset createResidue createUnit crossLink debugOff debugOn debugStatus deleteBond deleteOffLibEntry deleteRestraint desc deSelect displayPdbAtomMap displayPdbResMap edit flip groupSelectedAtoms help impose list listOff loadAmberParams loadAmberPrep loadMol2 loadOff loadPdb loadPdbUsingSeq logFile matchVariables measureGeom quit relax remove restrainAngle restrainBond restrainTorsion saveAmberParm saveAmberParmPert saveAmberParmPol saveAmberParmPolPertsaveAmberPrep saveMol2 saveOff saveOffParm savePdb scaleCharges select sequence set setBox solvateBox solvateCap solvateDontClip solvateOct solvateShell source transform translate verbosity zMatrix For a list of the current aliases, type "alias". > help saveamberparm saveAmberParm unit topologyfilename coordinatefilename UNIT _unit_ STRING _topologyfilename_ STRING _coordinatefilename_ Save the AMBER topology and coordinate files for the UNIT into the files named _topologyfilename_ and _coordinatefilename_ respectively. This command will cause LEaP to search its list of PARMSETs for parameters defining all of the interactions between the ATOMs within the UNIT. This command produces a topology file and a coordinate file which are identical in format to those produced by the AMBER program PARM, and which can be read into AMBER and SPASMS for energy minimization, dynamics, or nmode calculations. See also: saveAmberParmPol, saveAmberParmPert, and saveAmberParmPolPert for including atomic polarizabilities and preparing free energy perturbation calculations. > help saveamberparam No help available. > quit Quit log started: Mon Jun 4 17:19:22 2012 Log file: ./leap.log >>> # >>> # ----- leaprc for loading the ff10 force field >>> # ----- NOTE: this is designed for PDB format 3! >>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >>> # >>> # load atom type hybridizations >>> # >>> addAtomTypes { >>> { "H" "H" "sp3" } >>> { "HO" "H" "sp3" } >>> { "HS" "H" "sp3" } >>> { "H1" "H" "sp3" } >>> { "H2" "H" "sp3" } >>> { "H3" "H" "sp3" } >>> { "H4" "H" "sp3" } >>> { "H5" "H" "sp3" } >>> { "HW" "H" "sp3" } >>> { "HC" "H" "sp3" } >>> { "HA" "H" "sp3" } >>> { "HP" "H" "sp3" } >>> { "HZ" "H" "sp3" } >>> { "OH" "O" "sp3" } >>> { "OS" "O" "sp3" } >>> { "O" "O" "sp2" } >>> { "O2" "O" "sp2" } >>> { "OP" "O" "sp2" } >>> { "OW" "O" "sp3" } >>> { "CT" "C" "sp3" } >>> { "CX" "C" "sp3" } >>> { "CH" "C" "sp3" } >>> { "CS" "C" "sp2" } >>> { "C" "C" "sp2" } >>> { "C*" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CB" "C" "sp2" } >>> { "CC" "C" "sp2" } >>> { "CN" "C" "sp2" } >>> { "CM" "C" "sp2" } >>> { "CK" "C" "sp2" } >>> { "CQ" "C" "sp2" } >>> { "CD" "C" "sp2" } >>> { "C5" "C" "sp2" } >>> { "C4" "C" "sp2" } >>> { "CP" "C" "sp2" } >>> { "CI" "C" "sp3" } >>> { "CJ" "C" "sp2" } >>> { "CW" "C" "sp2" } >>> { "CV" "C" "sp2" } >>> { "CR" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CY" "C" "sp2" } >>> { "C0" "C" "sp2" } >>> { "MG" "Mg" "sp3" } >>> { "N" "N" "sp2" } >>> { "NA" "N" "sp2" } >>> { "N2" "N" "sp2" } >>> { "N*" "N" "sp2" } >>> { "NP" "N" "sp2" } >>> { "NQ" "N" "sp2" } >>> { "NB" "N" "sp2" } >>> { "NC" "N" "sp2" } >>> { "NT" "N" "sp3" } >>> { "NY" "N" "sp2" } >>> { "N3" "N" "sp3" } >>> { "S" "S" "sp3" } >>> { "SH" "S" "sp3" } >>> { "P" "P" "sp3" } >>> { "LP" "" "sp3" } >>> { "EP" "" "sp3" } >>> { "F" "F" "sp3" } >>> { "Cl" "Cl" "sp3" } >>> { "Br" "Br" "sp3" } >>> { "I" "I" "sp3" } >>> { "F-" "F" "sp3" } >>> { "Cl-" "Cl" "sp3" } >>> { "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" } >>> } addAtomTypes: type Cl- - max length is 2 addAtomTypes: type Br- - max length is 2 addAtomTypes: type Li+ - max length is 2 addAtomTypes: type Na+ - max length is 2 addAtomTypes: type Rb+ - max length is 2 addAtomTypes: type Cs+ - max length is 2 addAtomTypes: type Mg+ - max length is 2 >>> # >>> # Load the main parameter set. >>> # >>> parm10 = loadamberparams parm10.dat Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >>> # >>> # Load main chain and terminating amino acid libraries, nucleic acids >>> # >>> loadOff amino10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/amino10.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >>> loadOff aminoct10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminoct10.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >>> loadOff aminont10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminont10.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >>> loadOff nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/nucleic10.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: U Loading: U3 Loading: U5 Loading: UN >>> # >>> # Load water and ions >>> # >>> loadOff ions08.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >>> loadOff solvents.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >>> HOH = TP3 >>> WAT = TP3 >>> >>> # >>> # Define the PDB name map for the amino acids and nucleic acids >>> # >>> addPdbResMap { >>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >>> { 0 "G" "G5" } { 1 "G" "G3" } >>> { 0 "A" "A5" } { 1 "A" "A3" } >>> { 0 "C" "C5" } { 1 "C" "C3" } >>> { 0 "U" "U5" } { 1 "U" "U3" } >>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >>> # some old Amber residue names for RNA: >>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >>> # some really old Amber residue names, assuming DNA: >>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >>> # uncomment out the following if you have this old style RNA files: >>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >>> >>> } >>> >>> # try to be good about reading in really old atom names as well: >>> addPdbAtomMap { >>> { "O5*" "O5'" } >>> { "C5*" "C5'" } >>> { "C4*" "C4'" } >>> { "O4*" "O4'" } >>> { "C3*" "C3'" } >>> { "O3*" "O3'" } >>> { "C2*" "C2'" } >>> { "O2*" "O2'" } >>> { "C1*" "C1'" } >>> { "C5M" "C7" } >>> { "H1*" "H1'" } >>> { "H2*1" "H2'" } >>> { "H2*2" "H2''" } >>> { "H2'1" "H2'" } >>> { "H2'2" "H2''" } >>> { "H3*" "H3'" } >>> { "H4*" "H4'" } >>> { "H5*1" "H5'" } >>> { "H5*2" "H5''" } >>> { "H5'1" "H5'" } >>> { "H5'2" "H5''" } >>> { "HO'2" "HO2'" } >>> { "H5T" "HO5'" } >>> { "H3T" "HO3'" } >>> { "O1'" "O4'" } >>> { "OA" "OP1" } >>> { "OB" "OP2" } >>> { "O1P" "OP1" } >>> { "O2P" "OP2" } >>> } >>> >>> # >>> # assume that most often proteins use HIE >>> # >>> NHIS = NHIE >>> HIS = HIE >>> CHIS = CHIE >> >> >> # Extra constant pH libraries for Amino Acids >> loadOFF constph.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/constph.lib Loading: AS2 Loading: AS4 Loading: GL4 >> >> # Extra constant pH libraries for Nucleic Acids >> loadOFF all_prot_nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_prot_nucleic10.lib Loading: A3E Loading: A3P Loading: A5E Loading: A5P Loading: AE Loading: AP Loading: C3E Loading: C3P Loading: C5E Loading: C5P Loading: CE Loading: CP Loading: D3A Loading: D3AE Loading: D3C Loading: D3CE Loading: D3G Loading: D3GE Loading: D3T Loading: D3TE Loading: D5A Loading: D5AE Loading: D5C Loading: D5CE Loading: D5G Loading: D5GE Loading: D5T Loading: D5TE Loading: DAE Loading: DAP Loading: DCE Loading: DCP Loading: DGD Loading: DGE Loading: DTD Loading: DTE Loading: G3D Loading: G3E Loading: G5D Loading: G5E Loading: GD Loading: GE Loading: U3D Loading: U3E Loading: U5D Loading: U5E Loading: UD Loading: UE >> loadOFF cph_nucleic_caps.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/cph_nucleic_caps.lib Loading: CH3 Loading: MOC >> >> # Necessary constant pH force field modifications >> loadAmberParams frcmod.constph Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.constph Reading force field modification type file (frcmod) Reading title: Force field modifcations for titrations >> loadAmberParams frcmod.protonated_nucleic Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.protonated_nucleic Reading force field modification type file (frcmod) Reading title: Force field modifications for protonated nucleic acids (UNKNOWN ATOM TYPE: NX) (UNKNOWN ATOM TYPE: OX) (UNKNOWN ATOM TYPE: HD) >> >> # PBRadii must be mbondi2, corresponding to the proper reference energies >> set default PBRadii mbondi2 Using H(N)-modified Bondi radii > > > # Create blocked amino acid systems. > system = seq { ACE ASP NME } ERROR: syntax error saveamberparm system asp.prmtop asp.inpcrd saveAmberParm: Argument #1 is type String must be of type: [unit] usage: saveAmberParm > system ERROR: syntax error > fg ERROR: syntax error > quit Quit log started: Mon Jun 4 17:19:36 2012 Log file: ./leap.log >>> # >>> # ----- leaprc for loading the ff10 force field >>> # ----- NOTE: this is designed for PDB format 3! >>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >>> # >>> # load atom type hybridizations >>> # >>> addAtomTypes { >>> { "H" "H" "sp3" } >>> { "HO" "H" "sp3" } >>> { "HS" "H" "sp3" } >>> { "H1" "H" "sp3" } >>> { "H2" "H" "sp3" } >>> { "H3" "H" "sp3" } >>> { "H4" "H" "sp3" } >>> { "H5" "H" "sp3" } >>> { "HW" "H" "sp3" } >>> { "HC" "H" "sp3" } >>> { "HA" "H" "sp3" } >>> { "HP" "H" "sp3" } >>> { "HZ" "H" "sp3" } >>> { "OH" "O" "sp3" } >>> { "OS" "O" "sp3" } >>> { "O" "O" "sp2" } >>> { "O2" "O" "sp2" } >>> { "OP" "O" "sp2" } >>> { "OW" "O" "sp3" } >>> { "CT" "C" "sp3" } >>> { "CX" "C" "sp3" } >>> { "CH" "C" "sp3" } >>> { "CS" "C" "sp2" } >>> { "C" "C" "sp2" } >>> { "C*" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CB" "C" "sp2" } >>> { "CC" "C" "sp2" } >>> { "CN" "C" "sp2" } >>> { "CM" "C" "sp2" } >>> { "CK" "C" "sp2" } >>> { "CQ" "C" "sp2" } >>> { "CD" "C" "sp2" } >>> { "C5" "C" "sp2" } >>> { "C4" "C" "sp2" } >>> { "CP" "C" "sp2" } >>> { "CI" "C" "sp3" } >>> { "CJ" "C" "sp2" } >>> { "CW" "C" "sp2" } >>> { "CV" "C" "sp2" } >>> { "CR" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CY" "C" "sp2" } >>> { "C0" "C" "sp2" } >>> { "MG" "Mg" "sp3" } >>> { "N" "N" "sp2" } >>> { "NA" "N" "sp2" } >>> { "N2" "N" "sp2" } >>> { "N*" "N" "sp2" } >>> { "NP" "N" "sp2" } >>> { "NQ" "N" "sp2" } >>> { "NB" "N" "sp2" } >>> { "NC" "N" "sp2" } >>> { "NT" "N" "sp3" } >>> { "NY" "N" "sp2" } >>> { "N3" "N" "sp3" } >>> { "S" "S" "sp3" } >>> { "SH" "S" "sp3" } >>> { "P" "P" "sp3" } >>> { "LP" "" "sp3" } >>> { "EP" "" "sp3" } >>> { "F" "F" "sp3" } >>> { "Cl" "Cl" "sp3" } >>> { "Br" "Br" "sp3" } >>> { "I" "I" "sp3" } >>> { "F-" "F" "sp3" } >>> { "Cl-" "Cl" "sp3" } >>> { "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" } >>> } addAtomTypes: type Cl- - max length is 2 addAtomTypes: type Br- - max length is 2 addAtomTypes: type Li+ - max length is 2 addAtomTypes: type Na+ - max length is 2 addAtomTypes: type Rb+ - max length is 2 addAtomTypes: type Cs+ - max length is 2 addAtomTypes: type Mg+ - max length is 2 >>> # >>> # Load the main parameter set. >>> # >>> parm10 = loadamberparams parm10.dat Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >>> # >>> # Load main chain and terminating amino acid libraries, nucleic acids >>> # >>> loadOff amino10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/amino10.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >>> loadOff aminoct10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminoct10.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >>> loadOff aminont10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminont10.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >>> loadOff nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/nucleic10.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: U Loading: U3 Loading: U5 Loading: UN >>> # >>> # Load water and ions >>> # >>> loadOff ions08.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >>> loadOff solvents.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >>> HOH = TP3 >>> WAT = TP3 >>> >>> # >>> # Define the PDB name map for the amino acids and nucleic acids >>> # >>> addPdbResMap { >>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >>> { 0 "G" "G5" } { 1 "G" "G3" } >>> { 0 "A" "A5" } { 1 "A" "A3" } >>> { 0 "C" "C5" } { 1 "C" "C3" } >>> { 0 "U" "U5" } { 1 "U" "U3" } >>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >>> # some old Amber residue names for RNA: >>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >>> # some really old Amber residue names, assuming DNA: >>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >>> # uncomment out the following if you have this old style RNA files: >>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >>> >>> } >>> >>> # try to be good about reading in really old atom names as well: >>> addPdbAtomMap { >>> { "O5*" "O5'" } >>> { "C5*" "C5'" } >>> { "C4*" "C4'" } >>> { "O4*" "O4'" } >>> { "C3*" "C3'" } >>> { "O3*" "O3'" } >>> { "C2*" "C2'" } >>> { "O2*" "O2'" } >>> { "C1*" "C1'" } >>> { "C5M" "C7" } >>> { "H1*" "H1'" } >>> { "H2*1" "H2'" } >>> { "H2*2" "H2''" } >>> { "H2'1" "H2'" } >>> { "H2'2" "H2''" } >>> { "H3*" "H3'" } >>> { "H4*" "H4'" } >>> { "H5*1" "H5'" } >>> { "H5*2" "H5''" } >>> { "H5'1" "H5'" } >>> { "H5'2" "H5''" } >>> { "HO'2" "HO2'" } >>> { "H5T" "HO5'" } >>> { "H3T" "HO3'" } >>> { "O1'" "O4'" } >>> { "OA" "OP1" } >>> { "OB" "OP2" } >>> { "O1P" "OP1" } >>> { "O2P" "OP2" } >>> } >>> >>> # >>> # assume that most often proteins use HIE >>> # >>> NHIS = NHIE >>> HIS = HIE >>> CHIS = CHIE >> >> >> # Extra constant pH libraries for Amino Acids >> loadOFF constph.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/constph.lib Loading: AS2 Loading: AS4 Loading: GL4 >> >> # Extra constant pH libraries for Nucleic Acids >> loadOFF all_prot_nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_prot_nucleic10.lib Loading: A3E Loading: A3P Loading: A5E Loading: A5P Loading: AE Loading: AP Loading: C3E Loading: C3P Loading: C5E Loading: C5P Loading: CE Loading: CP Loading: D3A Loading: D3AE Loading: D3C Loading: D3CE Loading: D3G Loading: D3GE Loading: D3T Loading: D3TE Loading: D5A Loading: D5AE Loading: D5C Loading: D5CE Loading: D5G Loading: D5GE Loading: D5T Loading: D5TE Loading: DAE Loading: DAP Loading: DCE Loading: DCP Loading: DGD Loading: DGE Loading: DTD Loading: DTE Loading: G3D Loading: G3E Loading: G5D Loading: G5E Loading: GD Loading: GE Loading: U3D Loading: U3E Loading: U5D Loading: U5E Loading: UD Loading: UE >> loadOFF cph_nucleic_caps.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/cph_nucleic_caps.lib Loading: CH3 Loading: MOC >> >> # Necessary constant pH force field modifications >> loadAmberParams frcmod.constph Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.constph Reading force field modification type file (frcmod) Reading title: Force field modifcations for titrations >> loadAmberParams frcmod.protonated_nucleic Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.protonated_nucleic Reading force field modification type file (frcmod) Reading title: Force field modifications for protonated nucleic acids (UNKNOWN ATOM TYPE: NX) (UNKNOWN ATOM TYPE: OX) (UNKNOWN ATOM TYPE: HD) >> >> # PBRadii must be mbondi2, corresponding to the proper reference energies >> set default PBRadii mbondi2 Using H(N)-modified Bondi radii > > > # Create blocked amino acid systems. > system = seq { ACE ASP NME } ERROR: syntax error saveamberparm system asp.prmtop asp.inpcrd saveAmberParm: Argument #1 is type String must be of type: [unit] usage: saveAmberParm > help Help is available on the following subjects: _cmd_options_ _types_ add addAtomTypes addIons addIons2 addPath addPdbAtomMap addPdbResMap alias alignAxes bond bondByDistance center charge check clearPdbAtomMap clearPdbResMap clearVariables combine copy createAtom createParmset createResidue createUnit crossLink debugOff debugOn debugStatus deleteBond deleteOffLibEntry deleteRestraint desc deSelect displayPdbAtomMap displayPdbResMap edit flip groupSelectedAtoms help impose list listOff loadAmberParams loadAmberPrep loadMol2 loadOff loadPdb loadPdbUsingSeq logFile matchVariables measureGeom quit relax remove restrainAngle restrainBond restrainTorsion saveAmberParm saveAmberParmPert saveAmberParmPol saveAmberParmPolPertsaveAmberPrep saveMol2 saveOff saveOffParm savePdb scaleCharges select sequence set setBox solvateBox solvateCap solvateDontClip solvateOct solvateShell source transform translate verbosity zMatrix For a list of the current aliases, type "alias". > help seq No help available. > help sequence variable = sequence list LIST _list_ The sequence command is used to create a new UNIT by copying the contents of a LIST of UNITs. As each UNIT in the list is copied, a bond is created between its head atom and the tail ATOM of the previous UNIT, if both connect ATOMs are defined. If only one of the connect pair is defined, a warning is generated and no bond is created. If neither connection ATOM is defined then no bond is created. As each RESIDUE within a UNIT is copied, it is assigned a sequence number reflecting the order added. The order of RESIDUEs in multi-RESIDUE UNITs is maintained. This command builds reasonable starting coordinates for the new UNIT by assigning internal coordinates to the linkages between the component UNITs and building the Cartesian coordinates from these and the internal coordinates of the component UNITs. > quit Quit log started: Mon Jun 4 17:19:47 2012 Log file: ./leap.log >>> # >>> # ----- leaprc for loading the ff10 force field >>> # ----- NOTE: this is designed for PDB format 3! >>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >>> # >>> # load atom type hybridizations >>> # >>> addAtomTypes { >>> { "H" "H" "sp3" } >>> { "HO" "H" "sp3" } >>> { "HS" "H" "sp3" } >>> { "H1" "H" "sp3" } >>> { "H2" "H" "sp3" } >>> { "H3" "H" "sp3" } >>> { "H4" "H" "sp3" } >>> { "H5" "H" "sp3" } >>> { "HW" "H" "sp3" } >>> { "HC" "H" "sp3" } >>> { "HA" "H" "sp3" } >>> { "HP" "H" "sp3" } >>> { "HZ" "H" "sp3" } >>> { "OH" "O" "sp3" } >>> { "OS" "O" "sp3" } >>> { "O" "O" "sp2" } >>> { "O2" "O" "sp2" } >>> { "OP" "O" "sp2" } >>> { "OW" "O" "sp3" } >>> { "CT" "C" "sp3" } >>> { "CX" "C" "sp3" } >>> { "CH" "C" "sp3" } >>> { "CS" "C" "sp2" } >>> { "C" "C" "sp2" } >>> { "C*" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CB" "C" "sp2" } >>> { "CC" "C" "sp2" } >>> { "CN" "C" "sp2" } >>> { "CM" "C" "sp2" } >>> { "CK" "C" "sp2" } >>> { "CQ" "C" "sp2" } >>> { "CD" "C" "sp2" } >>> { "C5" "C" "sp2" } >>> { "C4" "C" "sp2" } >>> { "CP" "C" "sp2" } >>> { "CI" "C" "sp3" } >>> { "CJ" "C" "sp2" } >>> { "CW" "C" "sp2" } >>> { "CV" "C" "sp2" } >>> { "CR" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CY" "C" "sp2" } >>> { "C0" "C" "sp2" } >>> { "MG" "Mg" "sp3" } >>> { "N" "N" "sp2" } >>> { "NA" "N" "sp2" } >>> { "N2" "N" "sp2" } >>> { "N*" "N" "sp2" } >>> { "NP" "N" "sp2" } >>> { "NQ" "N" "sp2" } >>> { "NB" "N" "sp2" } >>> { "NC" "N" "sp2" } >>> { "NT" "N" "sp3" } >>> { "NY" "N" "sp2" } >>> { "N3" "N" "sp3" } >>> { "S" "S" "sp3" } >>> { "SH" "S" "sp3" } >>> { "P" "P" "sp3" } >>> { "LP" "" "sp3" } >>> { "EP" "" "sp3" } >>> { "F" "F" "sp3" } >>> { "Cl" "Cl" "sp3" } >>> { "Br" "Br" "sp3" } >>> { "I" "I" "sp3" } >>> { "F-" "F" "sp3" } >>> { "Cl-" "Cl" "sp3" } >>> { "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" } >>> } addAtomTypes: type Cl- - max length is 2 addAtomTypes: type Br- - max length is 2 addAtomTypes: type Li+ - max length is 2 addAtomTypes: type Na+ - max length is 2 addAtomTypes: type Rb+ - max length is 2 addAtomTypes: type Cs+ - max length is 2 addAtomTypes: type Mg+ - max length is 2 >>> # >>> # Load the main parameter set. >>> # >>> parm10 = loadamberparams parm10.dat Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >>> # >>> # Load main chain and terminating amino acid libraries, nucleic acids >>> # >>> loadOff amino10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/amino10.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >>> loadOff aminoct10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminoct10.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >>> loadOff aminont10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminont10.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >>> loadOff nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/nucleic10.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: U Loading: U3 Loading: U5 Loading: UN >>> # >>> # Load water and ions >>> # >>> loadOff ions08.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >>> loadOff solvents.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >>> HOH = TP3 >>> WAT = TP3 >>> >>> # >>> # Define the PDB name map for the amino acids and nucleic acids >>> # >>> addPdbResMap { >>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >>> { 0 "G" "G5" } { 1 "G" "G3" } >>> { 0 "A" "A5" } { 1 "A" "A3" } >>> { 0 "C" "C5" } { 1 "C" "C3" } >>> { 0 "U" "U5" } { 1 "U" "U3" } >>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >>> # some old Amber residue names for RNA: >>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >>> # some really old Amber residue names, assuming DNA: >>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >>> # uncomment out the following if you have this old style RNA files: >>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >>> >>> } >>> >>> # try to be good about reading in really old atom names as well: >>> addPdbAtomMap { >>> { "O5*" "O5'" } >>> { "C5*" "C5'" } >>> { "C4*" "C4'" } >>> { "O4*" "O4'" } >>> { "C3*" "C3'" } >>> { "O3*" "O3'" } >>> { "C2*" "C2'" } >>> { "O2*" "O2'" } >>> { "C1*" "C1'" } >>> { "C5M" "C7" } >>> { "H1*" "H1'" } >>> { "H2*1" "H2'" } >>> { "H2*2" "H2''" } >>> { "H2'1" "H2'" } >>> { "H2'2" "H2''" } >>> { "H3*" "H3'" } >>> { "H4*" "H4'" } >>> { "H5*1" "H5'" } >>> { "H5*2" "H5''" } >>> { "H5'1" "H5'" } >>> { "H5'2" "H5''" } >>> { "HO'2" "HO2'" } >>> { "H5T" "HO5'" } >>> { "H3T" "HO3'" } >>> { "O1'" "O4'" } >>> { "OA" "OP1" } >>> { "OB" "OP2" } >>> { "O1P" "OP1" } >>> { "O2P" "OP2" } >>> } >>> >>> # >>> # assume that most often proteins use HIE >>> # >>> NHIS = NHIE >>> HIS = HIE >>> CHIS = CHIE >> >> >> # Extra constant pH libraries for Amino Acids >> loadOFF constph.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/constph.lib Loading: AS2 Loading: AS4 Loading: GL4 >> >> # Extra constant pH libraries for Nucleic Acids >> loadOFF all_prot_nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_prot_nucleic10.lib Loading: A3E Loading: A3P Loading: A5E Loading: A5P Loading: AE Loading: AP Loading: C3E Loading: C3P Loading: C5E Loading: C5P Loading: CE Loading: CP Loading: D3A Loading: D3AE Loading: D3C Loading: D3CE Loading: D3G Loading: D3GE Loading: D3T Loading: D3TE Loading: D5A Loading: D5AE Loading: D5C Loading: D5CE Loading: D5G Loading: D5GE Loading: D5T Loading: D5TE Loading: DAE Loading: DAP Loading: DCE Loading: DCP Loading: DGD Loading: DGE Loading: DTD Loading: DTE Loading: G3D Loading: G3E Loading: G5D Loading: G5E Loading: GD Loading: GE Loading: U3D Loading: U3E Loading: U5D Loading: U5E Loading: UD Loading: UE >> loadOFF cph_nucleic_caps.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/cph_nucleic_caps.lib Loading: CH3 Loading: MOC >> >> # Necessary constant pH force field modifications >> loadAmberParams frcmod.constph Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.constph Reading force field modification type file (frcmod) Reading title: Force field modifcations for titrations >> loadAmberParams frcmod.protonated_nucleic Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.protonated_nucleic Reading force field modification type file (frcmod) Reading title: Force field modifications for protonated nucleic acids (UNKNOWN ATOM TYPE: NX) (UNKNOWN ATOM TYPE: OX) (UNKNOWN ATOM TYPE: HD) >> >> # PBRadii must be mbondi2, corresponding to the proper reference energies >> set default PBRadii mbondi2 Using H(N)-modified Bondi radii > > > # Create blocked amino acid systems. > system = sequence { ACE ASP NME } Sequence: ACE Sequence: ASP Joining ACE - ASP Sequence: NME Joining ASP - NME saveamberparm system asp.prmtop asp.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 5 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > system ERROR: syntax error > quit Quit log started: Mon Jun 4 17:22:02 2012 Log file: ./leap.log >>> # >>> # ----- leaprc for loading the ff10 force field >>> # ----- NOTE: this is designed for PDB format 3! >>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA >>> # >>> # load atom type hybridizations >>> # >>> addAtomTypes { >>> { "H" "H" "sp3" } >>> { "HO" "H" "sp3" } >>> { "HS" "H" "sp3" } >>> { "H1" "H" "sp3" } >>> { "H2" "H" "sp3" } >>> { "H3" "H" "sp3" } >>> { "H4" "H" "sp3" } >>> { "H5" "H" "sp3" } >>> { "HW" "H" "sp3" } >>> { "HC" "H" "sp3" } >>> { "HA" "H" "sp3" } >>> { "HP" "H" "sp3" } >>> { "HZ" "H" "sp3" } >>> { "OH" "O" "sp3" } >>> { "OS" "O" "sp3" } >>> { "O" "O" "sp2" } >>> { "O2" "O" "sp2" } >>> { "OP" "O" "sp2" } >>> { "OW" "O" "sp3" } >>> { "CT" "C" "sp3" } >>> { "CX" "C" "sp3" } >>> { "CH" "C" "sp3" } >>> { "CS" "C" "sp2" } >>> { "C" "C" "sp2" } >>> { "C*" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CB" "C" "sp2" } >>> { "CC" "C" "sp2" } >>> { "CN" "C" "sp2" } >>> { "CM" "C" "sp2" } >>> { "CK" "C" "sp2" } >>> { "CQ" "C" "sp2" } >>> { "CD" "C" "sp2" } >>> { "C5" "C" "sp2" } >>> { "C4" "C" "sp2" } >>> { "CP" "C" "sp2" } >>> { "CI" "C" "sp3" } >>> { "CJ" "C" "sp2" } >>> { "CW" "C" "sp2" } >>> { "CV" "C" "sp2" } >>> { "CR" "C" "sp2" } >>> { "CA" "C" "sp2" } >>> { "CY" "C" "sp2" } >>> { "C0" "C" "sp2" } >>> { "MG" "Mg" "sp3" } >>> { "N" "N" "sp2" } >>> { "NA" "N" "sp2" } >>> { "N2" "N" "sp2" } >>> { "N*" "N" "sp2" } >>> { "NP" "N" "sp2" } >>> { "NQ" "N" "sp2" } >>> { "NB" "N" "sp2" } >>> { "NC" "N" "sp2" } >>> { "NT" "N" "sp3" } >>> { "NY" "N" "sp2" } >>> { "N3" "N" "sp3" } >>> { "S" "S" "sp3" } >>> { "SH" "S" "sp3" } >>> { "P" "P" "sp3" } >>> { "LP" "" "sp3" } >>> { "EP" "" "sp3" } >>> { "F" "F" "sp3" } >>> { "Cl" "Cl" "sp3" } >>> { "Br" "Br" "sp3" } >>> { "I" "I" "sp3" } >>> { "F-" "F" "sp3" } >>> { "Cl-" "Cl" "sp3" } >>> { "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" } >>> } addAtomTypes: type Cl- - max length is 2 addAtomTypes: type Br- - max length is 2 addAtomTypes: type Li+ - max length is 2 addAtomTypes: type Na+ - max length is 2 addAtomTypes: type Rb+ - max length is 2 addAtomTypes: type Cs+ - max length is 2 addAtomTypes: type Mg+ - max length is 2 >>> # >>> # Load the main parameter set. >>> # >>> parm10 = loadamberparams parm10.dat Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >>> # >>> # Load main chain and terminating amino acid libraries, nucleic acids >>> # >>> loadOff amino10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/amino10.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >>> loadOff aminoct10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminoct10.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >>> loadOff aminont10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/aminont10.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >>> loadOff nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/nucleic10.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: G Loading: G3 Loading: G5 Loading: GN Loading: U Loading: U3 Loading: U5 Loading: UN >>> # >>> # Load water and ions >>> # >>> loadOff ions08.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/ions08.lib Loading: Br- Loading: Cl- Loading: Cs+ Loading: F- Loading: I- Loading: K+ Loading: Li+ Loading: Mg+ Loading: Na+ Loading: Rb+ >>> loadOff solvents.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >>> HOH = TP3 >>> WAT = TP3 >>> >>> # >>> # Define the PDB name map for the amino acids and nucleic acids >>> # >>> addPdbResMap { >>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >>> { 0 "G" "G5" } { 1 "G" "G3" } >>> { 0 "A" "A5" } { 1 "A" "A3" } >>> { 0 "C" "C5" } { 1 "C" "C3" } >>> { 0 "U" "U5" } { 1 "U" "U3" } >>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } >>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } >>> # some old Amber residue names for RNA: >>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } >>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } >>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } >>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } >>> # some really old Amber residue names, assuming DNA: >>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >>> # uncomment out the following if you have this old style RNA files: >>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } >>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } >>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } >>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } >>> >>> } >>> >>> # try to be good about reading in really old atom names as well: >>> addPdbAtomMap { >>> { "O5*" "O5'" } >>> { "C5*" "C5'" } >>> { "C4*" "C4'" } >>> { "O4*" "O4'" } >>> { "C3*" "C3'" } >>> { "O3*" "O3'" } >>> { "C2*" "C2'" } >>> { "O2*" "O2'" } >>> { "C1*" "C1'" } >>> { "C5M" "C7" } >>> { "H1*" "H1'" } >>> { "H2*1" "H2'" } >>> { "H2*2" "H2''" } >>> { "H2'1" "H2'" } >>> { "H2'2" "H2''" } >>> { "H3*" "H3'" } >>> { "H4*" "H4'" } >>> { "H5*1" "H5'" } >>> { "H5*2" "H5''" } >>> { "H5'1" "H5'" } >>> { "H5'2" "H5''" } >>> { "HO'2" "HO2'" } >>> { "H5T" "HO5'" } >>> { "H3T" "HO3'" } >>> { "O1'" "O4'" } >>> { "OA" "OP1" } >>> { "OB" "OP2" } >>> { "O1P" "OP1" } >>> { "O2P" "OP2" } >>> } >>> >>> # >>> # assume that most often proteins use HIE >>> # >>> NHIS = NHIE >>> HIS = HIE >>> CHIS = CHIE >> >> >> # Extra constant pH libraries for Amino Acids >> loadOFF constph.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/constph.lib Loading: AS2 Loading: AS4 Loading: GL4 >> >> # Extra constant pH libraries for Nucleic Acids >> loadOFF all_prot_nucleic10.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/all_prot_nucleic10.lib Loading: A3E Loading: A3P Loading: A5E Loading: A5P Loading: AE Loading: AP Loading: C3E Loading: C3P Loading: C5E Loading: C5P Loading: CE Loading: CP Loading: D3A Loading: D3AE Loading: D3C Loading: D3CE Loading: D3G Loading: D3GE Loading: D3T Loading: D3TE Loading: D5A Loading: D5AE Loading: D5C Loading: D5CE Loading: D5G Loading: D5GE Loading: D5T Loading: D5TE Loading: DAE Loading: DAP Loading: DCE Loading: DCP Loading: DGD Loading: DGE Loading: DTD Loading: DTE Loading: G3D Loading: G3E Loading: G5D Loading: G5E Loading: GD Loading: GE Loading: U3D Loading: U3E Loading: U5D Loading: U5E Loading: UD Loading: UE >> loadOFF cph_nucleic_caps.lib Loading library: /Users/jchodera.mobile/local/src/amber11/dat/leap/lib/cph_nucleic_caps.lib Loading: CH3 Loading: MOC >> >> # Necessary constant pH force field modifications >> loadAmberParams frcmod.constph Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.constph Reading force field modification type file (frcmod) Reading title: Force field modifcations for titrations >> loadAmberParams frcmod.protonated_nucleic Loading parameters: /Users/jchodera.mobile/local/src/amber11/dat/leap/parm/frcmod.protonated_nucleic Reading force field modification type file (frcmod) Reading title: Force field modifications for protonated nucleic acids (UNKNOWN ATOM TYPE: NX) (UNKNOWN ATOM TYPE: OX) (UNKNOWN ATOM TYPE: HD) >> >> # PBRadii must be mbondi2, corresponding to the proper reference energies >> set default PBRadii mbondi2 Using H(N)-modified Bondi radii > > > # Create blocked amino acid systems. > system = sequence { ACE AS4 NME } Sequence: ACE Sequence: AS4 Joining ACE - AS4 Sequence: NME Joining AS4 - NME > saveamberparm system asp.prmtop asp.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 7 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > > system = sequence { ACE GL4 NME } Sequence: ACE Sequence: GL4 Joining ACE - GL4 Sequence: NME Joining GL4 - NME > saveamberparm system glu.prmtop glu.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 7 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > > system = sequence { ACE HIP NME } Sequence: ACE Sequence: HIP Joining ACE - HIP Sequence: NME Joining HIP - NME > saveamberparm system his.prmtop his.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 9 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > > system = sequence { ACE LYS NME } Sequence: ACE Sequence: LYS Joining ACE - LYS Sequence: NME Joining LYS - NME > saveamberparm system lys.prmtop lys.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 4 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > > system = sequence { ACE TYR NME } Sequence: ACE Sequence: TYR Joining ACE - TYR Sequence: NME Joining TYR - NME > saveamberparm system tyr.prmtop tyr.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 10 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > > quit Quit