log started: Wed Mar 2 14:43:15 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the Cornell et al. 1994 topologies >> # with parm99 >> # assumes that any unspecified nucleic acids are RNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "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" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "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" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /usr/local/amber10/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /usr/local/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_amino94.lib Loading library: /usr/local/amber10/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: 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 all_aminoct94.lib Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct94.lib Loading: 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 all_aminont94.lib Loading library: /usr/local/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> # >> # Load ion library >> # >> loadOff ions94.lib Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /usr/local/amber10/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 RNA. >> # >> 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 "GUA" "RG5" } { 1 "GUA" "RG3" } { "GUA" "RG" } >> { 0 "ADE" "RA5" } { 1 "ADE" "RA3" } { "ADE" "RA" } >> { 0 "CYT" "RC5" } { 1 "CYT" "RC3" } { "CYT" "RC" } >> { 0 "URA" "RU5" } { 1 "URA" "RU3" } { "URA" "RU" } >> { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } >> { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } >> { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } >> { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } >> { 0 "C5" "RC5" } >> { 0 "G5" "RG5" } >> { 0 "A5" "RA5" } >> { 0 "U5" "RU5" } >> { 1 "C3" "RC3" } >> { 1 "G3" "RG3" } >> { 1 "A3" "RA3" } >> { 1 "U3" "RU3" } >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "O2*" "O2'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "H2'" "H2'1" } >> { "HO2'" "HO'2" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> { "H4*" "H4'" } >> { "H3*" "H3'" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "HO*2" "HO'2" } >> } >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE >> >> # translate RNA residue names: >> >> GUA = RG >> CYT = RC >> ADE = RA >> URA = RU > > source leaprc.ff99bs0 Could not open file leaprc.ff99bs0: not found > source leaprc.ff99bsc0 ----- Source: /usr/local/amber10/dat/leap/cmd/leaprc.ff99bsc0 ----- Source of /usr/local/amber10/dat/leap/cmd/leaprc.ff99bsc0 done >> logFile leap.log log started: Wed Mar 2 14:43:32 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field >> # using parmbsc0 for nucleic acids (assumed to be DNA) >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "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" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "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" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> { "EP" "" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /usr/local/amber10/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) >> frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) >> frcmodbsc0 = loadamberparams frcmod.parmbsc0 Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.parmbsc0 Reading force field modification type file (frcmod) Reading title: modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/ >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /usr/local/amber10/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries (i.e. ff94 libs) >> # >> loadOff all_amino94.lib Loading library: /usr/local/amber10/dat/leap/lib/all_amino94.lib Loading: ALA Loading: ARG Loading: ASH Loading: 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 all_aminoct94.lib Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct94.lib Loading: 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 all_aminont94.lib Loading library: /usr/local/amber10/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff DNA_CI.lib Loading library: /usr/local/amber10/dat/leap/lib/DNA_CI.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DC Loading: DC3 Loading: DC5 Loading: DG Loading: DG3 Loading: DG5 Loading: DT Loading: DT3 Loading: DT5 >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: MG2 Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /usr/local/amber10/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 DNA. >> # >> 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 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "DC" "DC5" } >> { 0 "DG" "DG5" } >> { 0 "DA" "DA5" } >> { 0 "DT" "DT5" } >> { 1 "DC" "DC3" } >> { 1 "DG" "DG3" } >> { 1 "DA" "DA3" } >> { 1 "DT" "DT3" } >> >> } Substituting map 0ALA -> NALA for 0ALA -> NALA Substituting map 1ALA -> CALA for 1ALA -> CALA Substituting map 0ARG -> NARG for 0ARG -> NARG Substituting map 1ARG -> CARG for 1ARG -> CARG Substituting map 0ASN -> NASN for 0ASN -> NASN Substituting map 1ASN -> CASN for 1ASN -> CASN Substituting map 0ASP -> NASP for 0ASP -> NASP Substituting map 1ASP -> CASP for 1ASP -> CASP Substituting map 0CYS -> NCYS for 0CYS -> NCYS Substituting map 1CYS -> CCYS for 1CYS -> CCYS Substituting map 0CYX -> NCYX for 0CYX -> NCYX Substituting map 1CYX -> CCYX for 1CYX -> CCYX Substituting map 0GLN -> NGLN for 0GLN -> NGLN Substituting map 1GLN -> CGLN for 1GLN -> CGLN Substituting map 0GLU -> NGLU for 0GLU -> NGLU Substituting map 1GLU -> CGLU for 1GLU -> CGLU Substituting map 0GLY -> NGLY for 0GLY -> NGLY Substituting map 1GLY -> CGLY for 1GLY -> CGLY Substituting map 0HID -> NHID for 0HID -> NHID Substituting map 1HID -> CHID for 1HID -> CHID Substituting map 0HIE -> NHIE for 0HIE -> NHIE Substituting map 1HIE -> CHIE for 1HIE -> CHIE Substituting map 0HIP -> NHIP for 0HIP -> NHIP Substituting map 1HIP -> CHIP for 1HIP -> CHIP Substituting map 0ILE -> NILE for 0ILE -> NILE Substituting map 1ILE -> CILE for 1ILE -> CILE Substituting map 0LEU -> NLEU for 0LEU -> NLEU Substituting map 1LEU -> CLEU for 1LEU -> CLEU Substituting map 0LYS -> NLYS for 0LYS -> NLYS Substituting map 1LYS -> CLYS for 1LYS -> CLYS Substituting map 0MET -> NMET for 0MET -> NMET Substituting map 1MET -> CMET for 1MET -> CMET Substituting map 0PHE -> NPHE for 0PHE -> NPHE Substituting map 1PHE -> CPHE for 1PHE -> CPHE Substituting map 0PRO -> NPRO for 0PRO -> NPRO Substituting map 1PRO -> CPRO for 1PRO -> CPRO Substituting map 0SER -> NSER for 0SER -> NSER Substituting map 1SER -> CSER for 1SER -> CSER Substituting map 0THR -> NTHR for 0THR -> NTHR Substituting map 1THR -> CTHR for 1THR -> CTHR Substituting map 0TRP -> NTRP for 0TRP -> NTRP Substituting map 1TRP -> CTRP for 1TRP -> CTRP Substituting map 0TYR -> NTYR for 0TYR -> NTYR Substituting map 1TYR -> CTYR for 1TYR -> CTYR Substituting map 0VAL -> NVAL for 0VAL -> NVAL Substituting map 1VAL -> CVAL for 1VAL -> CVAL Substituting map 0HIS -> NHIS for 0HIS -> NHIS Substituting map 1HIS -> CHIS for 1HIS -> CHIS Substituting map 0GUA -> DG5 for 0GUA -> RG5 Substituting map 1GUA -> DG3 for 1GUA -> RG3 Substituting map GUA -> DG for GUA -> RG Substituting map 0ADE -> DA5 for 0ADE -> RA5 Substituting map 1ADE -> DA3 for 1ADE -> RA3 Substituting map ADE -> DA for ADE -> RA Substituting map 0CYT -> DC5 for 0CYT -> RC5 Substituting map 1CYT -> DC3 for 1CYT -> RC3 Substituting map CYT -> DC for CYT -> RC Substituting map 0G -> DG5 for 0G -> RG5 Substituting map 1G -> DG3 for 1G -> RG3 Substituting map G -> DG for G -> RG Substituting map GN -> DGN for GN -> RGN Substituting map 0A -> DA5 for 0A -> RA5 Substituting map 1A -> DA3 for 1A -> RA3 Substituting map A -> DA for A -> RA Substituting map AN -> DAN for AN -> RAN Substituting map 0C -> DC5 for 0C -> RC5 Substituting map 1C -> DC3 for 1C -> RC3 Substituting map C -> DC for C -> RC Substituting map CN -> DCN for CN -> RCN >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H2'" "H2'1" } >> { "H2''" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> { "H5'" "H5'1" } >> { "H5''" "H5'2" } >> { "OP1" "O1P" } >> { "OP2" "O2P" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> } Substituting map O5* -> O5' for O5* -> O5' Substituting map C5* -> C5' for C5* -> C5' Substituting map C4* -> C4' for C4* -> C4' Substituting map O4* -> O4' for O4* -> O4' Substituting map C3* -> C3' for C3* -> C3' Substituting map O3* -> O3' for O3* -> O3' Substituting map C2* -> C2' for C2* -> C2' Substituting map C1* -> C1' for C1* -> C1' Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2'1 for H2*1 -> H2'1 Substituting map H2' -> H2'1 for H2' -> H2'1 Substituting map H3* -> H3' for H3* -> H3' Substituting map H4* -> H4' for H4* -> H4' Substituting map H5*1 -> H5'1 for H5*1 -> H5'1 Substituting map H5*2 -> H5'2 for H5*2 -> H5'2 >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadamberparams frcmod.ol.dat Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.ol.dat Reading force field modification type file (frcmod) Reading title: Original parameter file (UNKNOWN ATOM TYPE: C1) > loadamberprep PBG.prepin Loading Prep file: ./PBG.prepin Loaded UNIT: PBG > loadamberprep PSU.prepin Loading Prep file: ./PSU.prepin Loaded UNIT: PSU > loadamberprep MRG.prepin Loading Prep file: ./MRG.prepin Loaded UNIT: MRG > loadamberprep MRC.prepin Loading Prep file: ./MRC.prepin Loaded UNIT: MRC > loadamberparams PBG.frcmod Loading parameters: ./PBG.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberparams PSU.frcmod Loading parameters: ./PSU.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberparams MRC.frcmod Loading parameters: ./MRC.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadamberparams MRG.frcmod Loading parameters: ./MRG.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > set PBG head PBG.1.P > set PBG tail PBG.1.O3' > asl=loadpdb asl2.pdb Loading PDB file: ./asl2.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: PSU, Terminal/beginning, was not found in name map.) (Residue 1: PSU, Nonterminal, was not found in name map.) (Residue 2: RA, Nonterminal, was not found in name map.) (Residue 3: RG, Nonterminal, was not found in name map.) (Residue 4: RA, Nonterminal, was not found in name map.) (Residue 5: MRC, Nonterminal, was not found in name map.) (Residue 6: RU, Nonterminal, was not found in name map.) (Residue 7: MRG, Nonterminal, was not found in name map.) (Residue 8: RA, Nonterminal, was not found in name map.) (Residue 9: RA, Nonterminal, was not found in name map.) (Residue 10: PBG, Nonterminal, was not found in name map.) (Residue 11: RA, Nonterminal, was not found in name map.) (Residue 12: PSU, Nonterminal, was not found in name map.) (Residue 13: RC, Nonterminal, was not found in name map.) (Residue 14: RU, Nonterminal, was not found in name map.) (Residue 15: RA, Nonterminal, was not found in name map.) (Residue 16: RA3, Nonterminal, was not found in name map.) (Residue 17: RU5, Nonterminal, was not found in name map.) (Residue 18: RU, Nonterminal, was not found in name map.) (Residue 19: RC3, Terminal/last, was not found in name map.) Joining PSU - PSU Joining PSU - RA Joining RA - RG Joining RG - RA Joining RA - MRC Joining MRC - RU Joining RU - MRG Joining MRG - RA Joining RA - RA Joining RA - PBG Joining PBG - RA Joining RA - PSU Joining PSU - RC Joining RC - RU Joining RU - RA Joining RA - RA3 Starting new chain with RU5 Joining RU5 - RU Joining RU - RC3 total atoms in file: 675 > check asl Checking 'asl'.... ERROR: The unperturbed charge of the unit: -18.691700 is not integral. WARNING: The unperturbed charge of the unit: -18.691700 is not zero. Warning: Close contact of 1.651880 angstroms between .R.A and .R.A Checking parameters for unit 'asl'. Checking for bond parameters. Checking for angle parameters. check: Errors: 1 Warnings: 2 > edit asl Table Editor: Check table... Table Editor: The table has no errors and 0 warnings. Table Editor: Table has been 'saved' back to the program. > check asl Checking 'asl'.... WARNING: The unperturbed charge of the unit: -19.000000 is not zero. Warning: Close contact of 1.651880 angstroms between .R.A and .R.A Checking parameters for unit 'asl'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. > solvatebox asl TIP3PBOX 10 Solute vdw bounding box: 27.852 40.872 25.150 Total bounding box for atom centers: 47.852 60.872 45.150 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 3 y= 4 z= 3 Adding box at: x=0 y=0 z=0 Center of solvent box is: 18.774349, 28.161524, 18.774349 Adding box at: x=0 y=0 z=1 Center of solvent box is: 18.774349, 28.161524, 0.000000 Adding box at: x=0 y=0 z=2 Center of solvent box is: 18.774349, 28.161524, -18.774349 Adding box at: x=0 y=1 z=0 Center of solvent box is: 18.774349, 9.387175, 18.774349 Adding box at: x=0 y=1 z=1 Center of solvent box is: 18.774349, 9.387175, 0.000000 Adding box at: x=0 y=1 z=2 Center of solvent box is: 18.774349, 9.387175, -18.774349 Adding box at: x=0 y=2 z=0 Center of solvent box is: 18.774349, -9.387175, 18.774349 Adding box at: x=0 y=2 z=1 Center of solvent box is: 18.774349, -9.387175, 0.000000 Adding box at: x=0 y=2 z=2 Center of solvent box is: 18.774349, -9.387175, -18.774349 Adding box at: x=0 y=3 z=0 Center of solvent box is: 18.774349, -28.161524, 18.774349 Adding box at: x=0 y=3 z=1 Center of solvent box is: 18.774349, -28.161524, 0.000000 Adding box at: x=0 y=3 z=2 Center of solvent box is: 18.774349, -28.161524, -18.774349 Adding box at: x=1 y=0 z=0 Center of solvent box is: 0.000000, 28.161524, 18.774349 Adding box at: x=1 y=0 z=1 Center of solvent box is: 0.000000, 28.161524, 0.000000 Adding box at: x=1 y=0 z=2 Center of solvent box is: 0.000000, 28.161524, -18.774349 Adding box at: x=1 y=1 z=0 Center of solvent box is: 0.000000, 9.387175, 18.774349 Adding box at: x=1 y=1 z=1 Center of solvent box is: 0.000000, 9.387175, 0.000000 Adding box at: x=1 y=1 z=2 Center of solvent box is: 0.000000, 9.387175, -18.774349 Adding box at: x=1 y=2 z=0 Center of solvent box is: 0.000000, -9.387175, 18.774349 Adding box at: x=1 y=2 z=1 Center of solvent box is: 0.000000, -9.387175, 0.000000 Adding box at: x=1 y=2 z=2 Center of solvent box is: 0.000000, -9.387175, -18.774349 Adding box at: x=1 y=3 z=0 Center of solvent box is: 0.000000, -28.161524, 18.774349 Adding box at: x=1 y=3 z=1 Center of solvent box is: 0.000000, -28.161524, 0.000000 Adding box at: x=1 y=3 z=2 Center of solvent box is: 0.000000, -28.161524, -18.774349 Adding box at: x=2 y=0 z=0 Center of solvent box is: -18.774349, 28.161524, 18.774349 Adding box at: x=2 y=0 z=1 Center of solvent box is: -18.774349, 28.161524, 0.000000 Adding box at: x=2 y=0 z=2 Center of solvent box is: -18.774349, 28.161524, -18.774349 Adding box at: x=2 y=1 z=0 Center of solvent box is: -18.774349, 9.387175, 18.774349 Adding box at: x=2 y=1 z=1 Center of solvent box is: -18.774349, 9.387175, 0.000000 Adding box at: x=2 y=1 z=2 Center of solvent box is: -18.774349, 9.387175, -18.774349 Adding box at: x=2 y=2 z=0 Center of solvent box is: -18.774349, -9.387175, 18.774349 Adding box at: x=2 y=2 z=1 Center of solvent box is: -18.774349, -9.387175, 0.000000 Adding box at: x=2 y=2 z=2 Center of solvent box is: -18.774349, -9.387175, -18.774349 Adding box at: x=2 y=3 z=0 Center of solvent box is: -18.774349, -28.161524, 18.774349 Adding box at: x=2 y=3 z=1 Center of solvent box is: -18.774349, -28.161524, 0.000000 Adding box at: x=2 y=3 z=2 Center of solvent box is: -18.774349, -28.161524, -18.774349 Total vdw box size: 51.040 63.857 48.270 angstroms. Volume: 157324.199 A^3 Total mass 70921.200 amu, Density 0.749 g/cc Added 3570 residues. > addions asl Na+ 0 19 Na+ ions required to neutralize. Adding 19 counter ions to "asl" using 1A grid Total solute charge: -19.00 Max atom radius: 2.10 Grid extends from solute vdw + 5.07 to 11.17 Box: enclosing: -23.34 -29.83 -22.13 23.60 30.01 22.21 sized: 40.66 34.17 41.87 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 11.66% of box, grid points 30563 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in asl at (-2.71, -1.34, -13.14). (Replacing solvent molecule) Placed Na+ in asl at (7.83, -7.93, -13.05). (Replacing solvent molecule) Placed Na+ in asl at (-1.49, 8.00, 7.82). (Replacing solvent molecule) Placed Na+ in asl at (-6.73, 1.69, -8.82). (Replacing solvent molecule) Placed Na+ in asl at (-11.92, 1.14, 4.44). (Replacing solvent molecule) Placed Na+ in asl at (12.40, -13.14, -7.86). (Replacing solvent molecule) Placed Na+ in asl at (12.56, -4.19, 4.06). (Replacing solvent molecule) Placed Na+ in asl at (6.00, 13.12, 8.01). (Replacing solvent molecule) Placed Na+ in asl at (10.36, 8.95, -7.88). (Replacing solvent molecule) Placed Na+ in asl at (4.67, -20.68, 1.32). (Replacing solvent molecule) Placed Na+ in asl at (2.51, 2.89, 16.36). (Replacing solvent molecule) Placed Na+ in asl at (-12.78, -24.43, 8.01). (Replacing solvent molecule) Placed Na+ in asl at (15.05, -9.36, 8.38). (Replacing solvent molecule) Placed Na+ in asl at (16.06, 17.43, 5.63). (Replacing solvent molecule) Placed Na+ in asl at (-8.41, -9.82, 10.90). (Replacing solvent molecule) Placed Na+ in asl at (5.67, -1.77, -14.40). (Replacing solvent molecule) Placed Na+ in asl at (-0.07, 14.70, -10.21). (Replacing solvent molecule) Placed Na+ in asl at (-11.89, 0.91, -5.72). (Replacing solvent molecule) Placed Na+ in asl at (-8.05, -0.61, 11.46). Done adding ions. > saveamberparm asl asl.prmtop asl.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. old PREP-specified impropers: : C4 C6 C5 C1' : C5 N3 C4 O4 : N3 N1 C2 O2 : C5 H6 C6 N1 : C4 C6 C5 C1' : C5 N3 C4 O4 : N3 N1 C2 O2 : C5 H6 C6 N1 : N1 N3 C2 O2 : C5 N4 C4 N3 : C4 C6 C5 H5 : C5 H6 C6 N1 : C4 C8 N9 C1' : H8 N9 C8 N7 : C6 C4 C5 N7 : C5 N1 C6 O6 : N2 N1 C2 N3 : C5 N9 C4 N3 : C4 C8 N9 C1' : C5 N9 C4 N3 : C4 C2 N3 C10 : H8 N9 C8 N7 : C6 C4 C5 N7 : N7 C6 C5 C4 : C5 N1 C6 O6 : C6 C13 N1 C2 : N3 N1 C2 N2 : C13 C11 C12 N2 : C12 C14 C13 N1 : C16 O30 C17 O31 : C19 C16 N40 H10 : N40 O32 C19 O33 : C4 C6 C5 C1' : C5 N3 C4 O4 : N3 N1 C2 O2 : C5 H6 C6 N1 total 138 improper torsions applied 36 improper torsions in old prep form Building H-Bond parameters. 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 3551 ) (no restraints)