log started: Mon Sep 24 12:48:44 2007 Log file: ./leap.log > # > # ----- leaprc for loading the ff03 (Duan et al.) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "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" } > # things should be there > { "IM" "Cl" "sp3" } > { "IP" "Na" "sp3" } > { "Li" "Li" "sp3" } > { "K" "K" "sp3" } > { "Rb" "Rb" "sp3" } > { "Cs" "Cs" "sp3" } > { "Zn" "Zn" "sp3" } > { "IB" "Na" "sp3" } > # "new" types > { "H0" "H" "sp3" } > > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /prog/amber8/dat/leap/parm/parm99.dat (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) > frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /prog/amber8/dat/leap/parm/frcmod.ff03 Reading force field mod type file (frcmod) > > # > # Load water and ions > # > loadOff ions94.lib Loading library: /prog/amber8/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: /prog/amber8/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 > HOH = TP3 > WAT = TP3 > > # > # Load the existing 94 lib for nucleic acids and C- and N- terminal groups > # > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /prog/amber8/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_aminoct94.lib Loading library: /prog/amber8/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: /prog/amber8/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 all_amino03.lib Loading library: /prog/amber8/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: 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: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > > # > # 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 "C5" "DC5" } > { 0 "G5" "DG5" } > { 0 "A5" "DA5" } > { 0 "T5" "DT5" } > { 1 "C3" "DC3" } > { 1 "G3" "DG3" } > { 1 "A3" "DA3" } > { 1 "T3" "DT3" } > > } > > 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" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'1" } > { "H5*2" "H5'2" } > # old ff atom names -> new > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./leap_1_MNK.inp > source leaprc.ff03 ----- Source: /prog/amber8/dat/leap/cmd/leaprc.ff03 ----- Source of /prog/amber8/dat/leap/cmd/leaprc.ff03 done >> logFile leap.log log started: Mon Sep 24 12:48:44 2007 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff03 (Duan et al.) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "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" } >> # things should be there >> { "IM" "Cl" "sp3" } >> { "IP" "Na" "sp3" } >> { "Li" "Li" "sp3" } >> { "K" "K" "sp3" } >> { "Rb" "Rb" "sp3" } >> { "Cs" "Cs" "sp3" } >> { "Zn" "Zn" "sp3" } >> { "IB" "Na" "sp3" } >> # "new" types >> { "H0" "H" "sp3" } >> >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /prog/amber8/dat/leap/parm/parm99.dat (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: LP) >> frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /prog/amber8/dat/leap/parm/frcmod.ff03 Reading force field mod type file (frcmod) >> >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /prog/amber8/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: /prog/amber8/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> HOH = TP3 >> WAT = TP3 >> >> # >> # Load the existing 94 lib for nucleic acids and C- and N- terminal groups >> # >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /prog/amber8/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_aminoct94.lib Loading library: /prog/amber8/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: /prog/amber8/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 all_amino03.lib Loading library: /prog/amber8/dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: 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: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> >> # >> # 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 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "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 -> DG5 Substituting map 1GUA -> DG3 for 1GUA -> DG3 Substituting map GUA -> DG for GUA -> DG Substituting map 0ADE -> DA5 for 0ADE -> DA5 Substituting map 1ADE -> DA3 for 1ADE -> DA3 Substituting map ADE -> DA for ADE -> DA Substituting map 0CYT -> DC5 for 0CYT -> DC5 Substituting map 1CYT -> DC3 for 1CYT -> DC3 Substituting map CYT -> DC for CYT -> DC Substituting map 0THY -> DT5 for 0THY -> DT5 Substituting map 1THY -> DT3 for 1THY -> DT3 Substituting map THY -> DT for THY -> DT Substituting map 0G -> DG5 for 0G -> DG5 Substituting map 1G -> DG3 for 1G -> DG3 Substituting map G -> DG for G -> DG Substituting map GN -> DGN for GN -> DGN Substituting map 0A -> DA5 for 0A -> DA5 Substituting map 1A -> DA3 for 1A -> DA3 Substituting map A -> DA for A -> DA Substituting map AN -> DAN for AN -> DAN Substituting map 0C -> DC5 for 0C -> DC5 Substituting map 1C -> DC3 for 1C -> DC3 Substituting map C -> DC for C -> DC Substituting map CN -> DCN for CN -> DCN Substituting map 0T -> DT5 for 0T -> DT5 Substituting map 1T -> DT3 for 1T -> DT3 Substituting map T -> DT for T -> DT Substituting map TN -> DTN for TN -> DTN Substituting map 0C5 -> DC5 for 0C5 -> DC5 Substituting map 0G5 -> DG5 for 0G5 -> DG5 Substituting map 0A5 -> DA5 for 0A5 -> DA5 Substituting map 0T5 -> DT5 for 0T5 -> DT5 Substituting map 1C3 -> DC3 for 1C3 -> DC3 Substituting map 1G3 -> DG3 for 1G3 -> DG3 Substituting map 1A3 -> DA3 for 1A3 -> DA3 Substituting map 1T3 -> DT3 for 1T3 -> DT3 >> >> 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" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } 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 C5M -> C7 for C5M -> C7 Substituting map H1* -> H1' for H1* -> H1' Substituting map H2*1 -> H2'1 for H2*1 -> H2'1 Substituting map H2*2 -> H2'2 for H2*2 -> H2'2 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 Substituting map O1' -> O4' for O1' -> O4' Substituting map OA -> O1P for OA -> O1P Substituting map OB -> O2P for OB -> O2P >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > loadamberparams ../../Dati_LEAP/parm_copZ.dat Loading parameters: ../../Dati_LEAP/parm_copZ.dat Reading force field mod type file (frcmod) (UNKNOWN ATOM TYPE: CU) (UNKNOWN ATOM TYPE: NL) (UNKNOWN ATOM TYPE: NJ) (UNKNOWN ATOM TYPE: NK) (UNKNOWN ATOM TYPE: NM) (UNKNOWN ATOM TYPE: NN) (UNKNOWN ATOM TYPE: NR) (UNKNOWN ATOM TYPE: O9) > loadAmberPrep ../../Dati_LEAP/CU.prep Loading Prep file: ../../Dati_LEAP/CU.prep (UNKNOWN ATOM TYPE: CU) Loaded UNIT: CU > loadAmberPrep ../../Dati_LEAP/CYG.prep Loading Prep file: ../../Dati_LEAP/CYG.prep Loaded UNIT: CYG > MNK = loadPdb in.pdb Loading PDB file: ./in.pdb Matching PDB residue names to LEaP variables. Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. (Residue 1: PRO, Nonterminal, was not found in name map.) (Residue 2: LYS, Nonterminal, was not found in name map.) (Residue 3: HID, Nonterminal, was not found in name map.) (Residue 4: GLU, Nonterminal, was not found in name map.) (Residue 5: PHE, Nonterminal, was not found in name map.) (Residue 6: SER, Nonterminal, was not found in name map.) (Residue 7: VAL, Nonterminal, was not found in name map.) (Residue 8: ASP, Nonterminal, was not found in name map.) (Residue 9: MET, Nonterminal, was not found in name map.) (Residue 10: THR, Nonterminal, was not found in name map.) (Residue 11: CYG, Nonterminal, was not found in name map.) (Residue 12: GLY, Nonterminal, was not found in name map.) (Residue 13: GLY, Nonterminal, was not found in name map.) (Residue 14: CYS, Nonterminal, was not found in name map.) (Residue 15: ALA, Nonterminal, was not found in name map.) (Residue 16: GLU, Nonterminal, was not found in name map.) (Residue 17: ALA, Nonterminal, was not found in name map.) (Residue 18: VAL, Nonterminal, was not found in name map.) (Residue 19: SER, Nonterminal, was not found in name map.) (Residue 20: ARG, Nonterminal, was not found in name map.) (Residue 21: VAL, Nonterminal, was not found in name map.) (Residue 22: LEU, Nonterminal, was not found in name map.) (Residue 23: ASN, Nonterminal, was not found in name map.) (Residue 24: LYS, Nonterminal, was not found in name map.) (Residue 25: LEU, Nonterminal, was not found in name map.) (Residue 26: GLY, Nonterminal, was not found in name map.) (Residue 27: GLY, Nonterminal, was not found in name map.) (Residue 28: VAL, Nonterminal, was not found in name map.) (Residue 29: LYS, Nonterminal, was not found in name map.) (Residue 30: TYR, Nonterminal, was not found in name map.) (Residue 31: ASP, Nonterminal, was not found in name map.) (Residue 32: ILE, Nonterminal, was not found in name map.) (Residue 33: ASP, Nonterminal, was not found in name map.) (Residue 34: LEU, Nonterminal, was not found in name map.) (Residue 35: PRO, Nonterminal, was not found in name map.) (Residue 36: ASN, Nonterminal, was not found in name map.) (Residue 37: LYS, Nonterminal, was not found in name map.) (Residue 38: LYS, Nonterminal, was not found in name map.) (Residue 39: VAL, Nonterminal, was not found in name map.) (Residue 40: CYS, Nonterminal, was not found in name map.) (Residue 41: ILE, Nonterminal, was not found in name map.) (Residue 42: GLU, Nonterminal, was not found in name map.) (Residue 43: SER, Nonterminal, was not found in name map.) (Residue 44: GLU, Nonterminal, was not found in name map.) (Residue 45: HID, Nonterminal, was not found in name map.) (Residue 46: SER, Nonterminal, was not found in name map.) (Residue 47: MET, Nonterminal, was not found in name map.) (Residue 48: ASP, Nonterminal, was not found in name map.) (Residue 49: THR, Nonterminal, was not found in name map.) (Residue 50: LEU, Nonterminal, was not found in name map.) (Residue 51: LEU, Nonterminal, was not found in name map.) (Residue 52: ALA, Nonterminal, was not found in name map.) (Residue 53: THR, Nonterminal, was not found in name map.) (Residue 54: LEU, Nonterminal, was not found in name map.) (Residue 55: LYS, Nonterminal, was not found in name map.) (Residue 56: LYS, Nonterminal, was not found in name map.) (Residue 57: THR, Nonterminal, was not found in name map.) (Residue 58: GLY, Nonterminal, was not found in name map.) (Residue 59: LYS, Nonterminal, was not found in name map.) (Residue 60: THR, Nonterminal, was not found in name map.) (Residue 61: VAL, Nonterminal, was not found in name map.) (Residue 62: SER, Nonterminal, was not found in name map.) (Residue 63: TYR, Nonterminal, was not found in name map.) (Residue 64: LEU, Nonterminal, was not found in name map.) (Residue 65: GLY, Nonterminal, was not found in name map.) (Residue 66: LEU, Nonterminal, was not found in name map.) Mapped residue GLU, term: Terminal/last, seq. number: 67 to: CGLU. Mapped residue MET, term: Terminal/beginning, seq. number: 68 to: NMET. (Residue 69: ASP, Nonterminal, was not found in name map.) (Residue 70: PRO, Nonterminal, was not found in name map.) (Residue 71: SER, Nonterminal, was not found in name map.) (Residue 72: MET, Nonterminal, was not found in name map.) (Residue 73: GLY, Nonterminal, was not found in name map.) (Residue 74: VAL, Nonterminal, was not found in name map.) (Residue 75: ASN, Nonterminal, was not found in name map.) (Residue 76: SER, Nonterminal, was not found in name map.) (Residue 77: VAL, Nonterminal, was not found in name map.) (Residue 78: THR, Nonterminal, was not found in name map.) (Residue 79: ILE, Nonterminal, was not found in name map.) (Residue 80: SER, Nonterminal, was not found in name map.) (Residue 81: VAL, Nonterminal, was not found in name map.) (Residue 82: GLU, Nonterminal, was not found in name map.) (Residue 83: GLY, Nonterminal, was not found in name map.) (Residue 84: MET, Nonterminal, was not found in name map.) (Residue 85: THR, Nonterminal, was not found in name map.) (Residue 86: CYG, Nonterminal, was not found in name map.) (Residue 87: ASN, Nonterminal, was not found in name map.) (Residue 88: SER, Nonterminal, was not found in name map.) (Residue 89: CYG, Nonterminal, was not found in name map.) (Residue 90: VAL, Nonterminal, was not found in name map.) (Residue 91: TRP, Nonterminal, was not found in name map.) (Residue 92: THR, Nonterminal, was not found in name map.) (Residue 93: ILE, Nonterminal, was not found in name map.) (Residue 94: GLU, Nonterminal, was not found in name map.) (Residue 95: GLN, Nonterminal, was not found in name map.) (Residue 96: GLN, Nonterminal, was not found in name map.) (Residue 97: ILE, Nonterminal, was not found in name map.) (Residue 98: GLY, Nonterminal, was not found in name map.) (Residue 99: LYS, Nonterminal, was not found in name map.) (Residue 100: VAL, Nonterminal, was not found in name map.) (Residue 101: ASN, Nonterminal, was not found in name map.) (Residue 102: GLY, Nonterminal, was not found in name map.) (Residue 103: VAL, Nonterminal, was not found in name map.) (Residue 104: HID, Nonterminal, was not found in name map.) (Residue 105: HID, Nonterminal, was not found in name map.) (Residue 106: ILE, Nonterminal, was not found in name map.) (Residue 107: LYS, Nonterminal, was not found in name map.) (Residue 108: VAL, Nonterminal, was not found in name map.) (Residue 109: SER, Nonterminal, was not found in name map.) (Residue 110: LEU, Nonterminal, was not found in name map.) (Residue 111: GLU, Nonterminal, was not found in name map.) (Residue 112: GLU, Nonterminal, was not found in name map.) (Residue 113: LYS, Nonterminal, was not found in name map.) (Residue 114: ASN, Nonterminal, was not found in name map.) (Residue 115: ALA, Nonterminal, was not found in name map.) (Residue 116: THR, Nonterminal, was not found in name map.) (Residue 117: ILE, Nonterminal, was not found in name map.) (Residue 118: ILE, Nonterminal, was not found in name map.) (Residue 119: TYR, Nonterminal, was not found in name map.) (Residue 120: ASP, Nonterminal, was not found in name map.) (Residue 121: PRO, Nonterminal, was not found in name map.) (Residue 122: LYS, Nonterminal, was not found in name map.) (Residue 123: LEU, Nonterminal, was not found in name map.) (Residue 124: GLN, Nonterminal, was not found in name map.) (Residue 125: THR, Nonterminal, was not found in name map.) (Residue 126: PRO, Nonterminal, was not found in name map.) (Residue 127: LYS, Nonterminal, was not found in name map.) (Residue 128: THR, Nonterminal, was not found in name map.) (Residue 129: LEU, Nonterminal, was not found in name map.) (Residue 130: GLN, Nonterminal, was not found in name map.) (Residue 131: GLU, Nonterminal, was not found in name map.) (Residue 132: ALA, Nonterminal, was not found in name map.) (Residue 133: ILE, Nonterminal, was not found in name map.) (Residue 134: ASP, Nonterminal, was not found in name map.) (Residue 135: ASP, Nonterminal, was not found in name map.) (Residue 136: MET, Nonterminal, was not found in name map.) (Residue 137: GLY, Nonterminal, was not found in name map.) (Residue 138: PHE, Nonterminal, was not found in name map.) (Residue 139: ASP, Nonterminal, was not found in name map.) (Residue 140: ALA, Nonterminal, was not found in name map.) (Residue 141: VAL, Nonterminal, was not found in name map.) (Residue 142: ILE, Nonterminal, was not found in name map.) (Residue 143: HID, Nonterminal, was not found in name map.) (Residue 144: ASN, Nonterminal, was not found in name map.) (Residue 145: PRO, Nonterminal, was not found in name map.) Mapped residue ASP, term: Terminal/last, seq. number: 146 to: CASP. (Residue 147: CU, Terminal/last, was not found in name map.) Joining NMET - PRO Joining PRO - LYS Joining LYS - HID Joining HID - GLU Joining GLU - PHE Joining PHE - SER Joining SER - VAL Joining VAL - ASP Joining ASP - MET Joining MET - THR Joining THR - CYG Joining CYG - GLY Joining GLY - GLY Joining GLY - CYS Joining CYS - ALA Joining ALA - GLU Joining GLU - ALA Joining ALA - VAL Joining VAL - SER Joining SER - ARG Joining ARG - VAL Joining VAL - LEU Joining LEU - ASN Joining ASN - LYS Joining LYS - LEU Joining LEU - GLY Joining GLY - GLY Joining GLY - VAL Joining VAL - LYS Joining LYS - TYR Joining TYR - ASP Joining ASP - ILE Joining ILE - ASP Joining ASP - LEU Joining LEU - PRO Joining PRO - ASN Joining ASN - LYS Joining LYS - LYS Joining LYS - VAL Joining VAL - CYS Joining CYS - ILE Joining ILE - GLU Joining GLU - SER Joining SER - GLU Joining GLU - HID Joining HID - SER Joining SER - MET Joining MET - ASP Joining ASP - THR Joining THR - LEU Joining LEU - LEU Joining LEU - ALA Joining ALA - THR Joining THR - LEU Joining LEU - LYS Joining LYS - LYS Joining LYS - THR Joining THR - GLY Joining GLY - LYS Joining LYS - THR Joining THR - VAL Joining VAL - SER Joining SER - TYR Joining TYR - LEU Joining LEU - GLY Joining GLY - LEU Joining LEU - CGLU Joining NMET - ASP Joining ASP - PRO Joining PRO - SER Joining SER - MET Joining MET - GLY Joining GLY - VAL Joining VAL - ASN Joining ASN - SER Joining SER - VAL Joining VAL - THR Joining THR - ILE Joining ILE - SER Joining SER - VAL Joining VAL - GLU Joining GLU - GLY Joining GLY - MET Joining MET - THR Joining THR - CYG Joining CYG - ASN Joining ASN - SER Joining SER - CYG Joining CYG - VAL Joining VAL - TRP Joining TRP - THR Joining THR - ILE Joining ILE - GLU Joining GLU - GLN Joining GLN - GLN Joining GLN - ILE Joining ILE - GLY Joining GLY - LYS Joining LYS - VAL Joining VAL - ASN Joining ASN - GLY Joining GLY - VAL Joining VAL - HID Joining HID - HID Joining HID - ILE Joining ILE - LYS Joining LYS - VAL Joining VAL - SER Joining SER - LEU Joining LEU - GLU Joining GLU - GLU Joining GLU - LYS Joining LYS - ASN Joining ASN - ALA Joining ALA - THR Joining THR - ILE Joining ILE - ILE Joining ILE - TYR Joining TYR - ASP Joining ASP - PRO Joining PRO - LYS Joining LYS - LEU Joining LEU - GLN Joining GLN - THR Joining THR - PRO Joining PRO - LYS Joining LYS - THR Joining THR - LEU Joining LEU - GLN Joining GLN - GLU Joining GLU - ALA Joining ALA - ILE Joining ILE - ASP Joining ASP - ASP Joining ASP - MET Joining MET - GLY Joining GLY - PHE Joining PHE - ASP Joining ASP - ALA Joining ALA - VAL Joining VAL - ILE Joining ILE - HID Joining HID - ASN Joining ASN - PRO Joining PRO - CASP total atoms in file: 1120 Leap added 1124 missing atoms according to residue templates: 1124 H / lone pairs > bond MNK.148.CU MNK.12.SG > bond MNK.148.CU MNK.87.SG > bond MNK.148.CU MNK.90.SG > > addions MNK Na+ 6 Adding 6 counter ions to "MNK" using 1A grid Total solute charge: -7.70 Max atom radius: 2.00 Grid extends from solute vdw + 1.87 to 7.87 Box: enclosing: -17.13 -15.70 -35.77 33.91 38.99 31.20 sized: 110.87 112.30 92.23 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 0 sec Volume = 2.02% of box, grid points 42303 (no solvent present) Calculating grid charges charges: 5 sec Placed Na+ in MNK at (12.87, 4.30, 21.23). Placed Na+ in MNK at (-1.13, 14.30, 4.23). Placed Na+ in MNK at (7.87, 23.30, -24.77). Placed Na+ in MNK at (-2.13, -0.70, -17.77). Placed Na+ in MNK at (5.87, -7.70, 16.23). Placed Na+ in MNK at (5.87, 14.30, -30.77). Done adding ions. > saveAmberParm MNK prm_1.top prm_1.crd Checking Unit. WARNING: There is a bond of 3.363639 angstroms between: ------- .R.A and .R.A ERROR: The unperturbed charge of the unit: -1.698000 is not integral. WARNING: The unperturbed charge of the unit: -1.698000 is not zero. -- ignoring the error and warnings. 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 C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 old PREP-specified impropers: : -M CA N H : CA +M C O : -M CA N H : CA +M C O : -M CA N H : CA +M C O total 395 improper torsions applied 6 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 CASP 1 CGLU 1 NMET 2 ) (no restraints) > savepdb MNK prm_1.pdb Writing pdb file: prm_1.pdb Shortening residue name for PDB format: NMET -> MET Shortening residue name for PDB format: CGLU -> GLU Shortening residue name for PDB format: NMET -> MET Shortening residue name for PDB format: CASP -> ASP > > quit Quit