log started: Thu Apr 28 10:29:56 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: /home/PraYagRaj/amber14/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: 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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> # >> # Define the PDB name map for the amino acids and 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 oldff/leaprc.ff99bsc0 ----- Source: /home/PraYagRaj/amber14/dat/leap/cmd/oldff/leaprc.ff99bsc0 ----- Source of /home/PraYagRaj/amber14/dat/leap/cmd/oldff/leaprc.ff99bsc0 done >> logFile leap.log log started: Thu Apr 28 10:30:16 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field >> # using parmbsc0 for nucleic acid. >> # ----- NOTE: this is designed for PDB format 3! >> # >> # 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" } >> { "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" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "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: /home/PraYagRaj/amber14/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: 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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/dat/leap/lib/DNA_CI.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 >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and 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" "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 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 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 -> RG5 for 0G -> RG5 Substituting map 1G -> RG3 for 1G -> RG3 Substituting map G -> RG for G -> RG Substituting map GN -> RGN for GN -> RGN Substituting map 0A -> RA5 for 0A -> RA5 Substituting map 1A -> RA3 for 1A -> RA3 Substituting map A -> RA for A -> RA Substituting map AN -> RAN for AN -> RAN Substituting map 0C -> RC5 for 0C -> RC5 Substituting map 1C -> RC3 for 1C -> RC3 Substituting map C -> RC for C -> RC Substituting map CN -> RCN for CN -> RCN Substituting map 0U -> RU5 for 0U -> RU5 Substituting map 1U -> RU3 for 1U -> RU3 Substituting map U -> RU for U -> RU Substituting map UN -> RUN for UN -> RUN >> >> 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" "H2'1" } >> { "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" } >> { "HO2'" "HO'2" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "OP1" "O1P" } >> { "OP2" "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 O2* -> O2' for O2* -> O2' 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 Substituting map HO2' -> HO'2 for HO2' -> HO'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 parm99bsc0SBgaff.dat Loading parameters: ./parm99bsc0SBgaff.dat Reading title: Merge of parm99.dat, gaff.dat, frcmod.ff99SB and frcmod.parmbsc0 (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) (UNKNOWN ATOM TYPE: hn) (UNKNOWN ATOM TYPE: hx) (UNKNOWN ATOM TYPE: c1) (UNKNOWN ATOM TYPE: cu) (UNKNOWN ATOM TYPE: cx) (UNKNOWN ATOM TYPE: n1) (UNKNOWN ATOM TYPE: n4) (UNKNOWN ATOM TYPE: nd) (UNKNOWN ATOM TYPE: ne) (UNKNOWN ATOM TYPE: nf) (UNKNOWN ATOM TYPE: nh) (UNKNOWN ATOM TYPE: no) (UNKNOWN ATOM TYPE: s2) (UNKNOWN ATOM TYPE: s4) (UNKNOWN ATOM TYPE: s6) (UNKNOWN ATOM TYPE: sx) (UNKNOWN ATOM TYPE: sy) (UNKNOWN ATOM TYPE: ss) (UNKNOWN ATOM TYPE: p2) (UNKNOWN ATOM TYPE: p3) (UNKNOWN ATOM TYPE: p4) (UNKNOWN ATOM TYPE: p5) (UNKNOWN ATOM TYPE: pb) (UNKNOWN ATOM TYPE: px) (UNKNOWN ATOM TYPE: py) > source leaprc.modrna08 ----- Source: /home/PraYagRaj/amber14/dat/leap/cmd/leaprc.modrna08 ----- Source of /home/PraYagRaj/amber14/dat/leap/cmd/leaprc.modrna08 done >> # >> # ----- leaprc for loading modified RNA nucleotides. The parameters are >> # described here: >> >> # R. Aduri, B.T. Psciuk, P. Saro, H. Taniga, >> # Schlegel, H.B. and J. SantaLucia, Jr. AMBER force field parameters >> # for the naturally occurring modified nucleosides in RNA. >> # J. Chem. Theory Comput. 3, 1465-1475, 2007. >> # >> # To use these residues, load this file into leap, after the Amber-FF, e.g.: >> # >> # > source leaprc.ff13SB >> # > source leaprc.modrna08 >> # >> >> modrna08 = loadAmberParams all_modrna08.frcmod Loading parameters: /home/PraYagRaj/amber14/dat/leap/parm/all_modrna08.frcmod Reading force field modification type file (frcmod) Reading title: parameters for the 107 modified nucleosides in RNA: see ../cmd/leaprc.modrna08 (UNKNOWN ATOM TYPE: CZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: SO) (UNKNOWN ATOM TYPE: SS) >> loadOff all_modrna08.lib Loading library: /home/PraYagRaj/amber14/dat/leap/lib/all_modrna08.lib Loading: 13P Loading: 1MA Loading: 1MG Loading: 1MI Loading: 1MP Loading: 26A Loading: 27G Loading: 2MA Loading: 2MG Loading: 2RG Loading: 2SC Loading: 2SU Loading: 3AU Loading: 3MC Loading: 3MP Loading: 3MU Loading: 4AC Loading: 4MC Loading: 4SU Loading: 52U Loading: 5AU Loading: 5CU Loading: 5DU Loading: 5FC Loading: 5HU Loading: 5MC Loading: 5MU Loading: 5TU Loading: 66A Loading: 6AA Loading: 6GA Loading: 6IA Loading: 6MA Loading: 6TA Loading: 7MG Loading: BCU Loading: BUG Loading: CMU Loading: DAG Loading: DHU Loading: DMA Loading: DMG Loading: DMU Loading: DWG Loading: EQG Loading: ESU Loading: HCU Loading: HIA Loading: HMC Loading: HNA Loading: HWG Loading: INO Loading: IWG Loading: K2C Loading: M1G Loading: M2A Loading: M3U Loading: M4C Loading: MAC Loading: MAU Loading: MCU Loading: MEU Loading: MFC Loading: MMA Loading: MMC Loading: MMG Loading: MMI Loading: MMU Loading: MRA Loading: MRC Loading: MRG Loading: MRI Loading: MRP Loading: MRU Loading: MSU Loading: MTA Loading: MTG Loading: N2G Loading: OAU Loading: OCU Loading: OEU Loading: OMU Loading: PBG Loading: PSU Loading: QGG Loading: QMG Loading: QUG Loading: SAU Loading: SCU Loading: SEU Loading: SIA Loading: SMA Loading: SMU Loading: SPA Loading: STA Loading: STU Loading: WBG Loading: WMG Loading: WYG > > asl=loadpdb trna1.pdb Loading PDB file: ./trna1.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue G, term: Terminal/beginning, seq. number: 0 to: RG5. Mapped residue C, term: Nonterminal, seq. number: 1 to: RC. Mapped residue G, term: Nonterminal, seq. number: 2 to: RG. Mapped residue G, term: Nonterminal, seq. number: 3 to: RG. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue U, term: Nonterminal, seq. number: 5 to: RU. Mapped residue U, term: Nonterminal, seq. number: 6 to: RU. Mapped residue U, term: Nonterminal, seq. number: 7 to: RU. Mapped residue A, term: Nonterminal, seq. number: 8 to: RA. (Residue 9: 2MG, Nonterminal, was not found in name map.) Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue U, term: Nonterminal, seq. number: 11 to: RU. Mapped residue C, term: Nonterminal, seq. number: 12 to: RC. Mapped residue A, term: Nonterminal, seq. number: 13 to: RA. Mapped residue G, term: Nonterminal, seq. number: 14 to: RG. (Residue 15: DHU, Nonterminal, was not found in name map.) (Residue 16: DHU, Nonterminal, was not found in name map.) Mapped residue G, term: Nonterminal, seq. number: 17 to: RG. Mapped residue G, term: Nonterminal, seq. number: 18 to: RG. Mapped residue G, term: Nonterminal, seq. number: 19 to: RG. Mapped residue A, term: Nonterminal, seq. number: 20 to: RA. Mapped residue G, term: Nonterminal, seq. number: 21 to: RG. Mapped residue A, term: Nonterminal, seq. number: 22 to: RA. Mapped residue G, term: Nonterminal, seq. number: 23 to: RG. Mapped residue C, term: Nonterminal, seq. number: 24 to: RC. Mapped residue G, term: Nonterminal, seq. number: 25 to: RG. Mapped residue C, term: Nonterminal, seq. number: 26 to: RC. Mapped residue C, term: Nonterminal, seq. number: 27 to: RC. Mapped residue A, term: Nonterminal, seq. number: 28 to: RA. Mapped residue G, term: Nonterminal, seq. number: 29 to: RG. Mapped residue A, term: Nonterminal, seq. number: 30 to: RA. Mapped residue C, term: Nonterminal, seq. number: 31 to: RC. Mapped residue U, term: Nonterminal, seq. number: 32 to: RU. Mapped residue G, term: Nonterminal, seq. number: 33 to: RG. Mapped residue A, term: Nonterminal, seq. number: 34 to: RA. Mapped residue A, term: Nonterminal, seq. number: 35 to: RA. Mapped residue G, term: Nonterminal, seq. number: 36 to: RG. Mapped residue A, term: Nonterminal, seq. number: 37 to: RA. Mapped residue U, term: Nonterminal, seq. number: 38 to: RU. Mapped residue C, term: Nonterminal, seq. number: 39 to: RC. Mapped residue U, term: Nonterminal, seq. number: 40 to: RU. Mapped residue G, term: Nonterminal, seq. number: 41 to: RG. Mapped residue G, term: Nonterminal, seq. number: 42 to: RG. Mapped residue A, term: Nonterminal, seq. number: 43 to: RA. Mapped residue G, term: Nonterminal, seq. number: 44 to: RG. Mapped residue G, term: Nonterminal, seq. number: 45 to: RG. Mapped residue U, term: Nonterminal, seq. number: 46 to: RU. Mapped residue C, term: Nonterminal, seq. number: 47 to: RC. Mapped residue C, term: Nonterminal, seq. number: 48 to: RC. Mapped residue U, term: Nonterminal, seq. number: 49 to: RU. Mapped residue G, term: Nonterminal, seq. number: 50 to: RG. Mapped residue U, term: Nonterminal, seq. number: 51 to: RU. Mapped residue G, term: Nonterminal, seq. number: 52 to: RG. Mapped residue U, term: Nonterminal, seq. number: 53 to: RU. (Residue 54: PSU, Nonterminal, was not found in name map.) Mapped residue C, term: Nonterminal, seq. number: 55 to: RC. Mapped residue G, term: Nonterminal, seq. number: 56 to: RG. Mapped residue A, term: Nonterminal, seq. number: 57 to: RA. Mapped residue U, term: Nonterminal, seq. number: 58 to: RU. Mapped residue C, term: Nonterminal, seq. number: 59 to: RC. Mapped residue C, term: Nonterminal, seq. number: 60 to: RC. Mapped residue A, term: Nonterminal, seq. number: 61 to: RA. Mapped residue C, term: Nonterminal, seq. number: 62 to: RC. Mapped residue A, term: Nonterminal, seq. number: 63 to: RA. Mapped residue G, term: Nonterminal, seq. number: 64 to: RG. Mapped residue A, term: Nonterminal, seq. number: 65 to: RA. Mapped residue A, term: Nonterminal, seq. number: 66 to: RA. Mapped residue U, term: Nonterminal, seq. number: 67 to: RU. Mapped residue U, term: Nonterminal, seq. number: 68 to: RU. Mapped residue C, term: Nonterminal, seq. number: 69 to: RC. Mapped residue G, term: Nonterminal, seq. number: 70 to: RG. Mapped residue C, term: Nonterminal, seq. number: 71 to: RC. Mapped residue A, term: Nonterminal, seq. number: 72 to: RA. Mapped residue C, term: Nonterminal, seq. number: 73 to: RC. Mapped residue C, term: Nonterminal, seq. number: 74 to: RC. Mapped residue A, term: Terminal/last, seq. number: 75 to: RA3. Joining RG5 - RC Joining RC - RG Joining RG - RG Joining RG - RA Joining RA - RU Joining RU - RU Joining RU - RU Joining RU - RA Joining RA - 2MG Joining 2MG - RC Joining RC - RU Joining RU - RC Joining RC - RA Joining RA - RG Joining RG - DHU Joining DHU - DHU Joining DHU - RG Joining RG - RG Joining RG - RG Joining RG - RA Joining RA - RG Joining RG - RA Joining RA - RG Joining RG - RC Joining RC - RG Joining RG - RC Joining RC - RC Joining RC - RA Joining RA - RG Joining RG - RA Joining RA - RC Joining RC - RU Joining RU - RG Joining RG - RA Joining RA - RA Joining RA - RG Joining RG - RA Joining RA - RU Joining RU - RC Joining RC - RU Joining RU - RG Joining RG - RG Joining RG - RA Joining RA - RG Joining RG - RG Joining RG - RU Joining RU - RC Joining RC - RC Joining RC - RU Joining RU - RG Joining RG - RU Joining RU - RG Joining RG - RU Joining RU - PSU Joining PSU - RC Joining RC - RG Joining RG - RA Joining RA - RU Joining RU - RC Joining RC - RC Joining RC - RA Joining RA - RC Joining RC - RA Joining RA - RG Joining RG - RA Joining RA - RA Joining RA - RU Joining RU - RU Joining RU - RC Joining RC - RG Joining RG - RC Joining RC - RA Joining RA - RC Joining RC - RC Joining RC - RA3 total atoms in file: 1630 Leap added 820 missing atoms according to residue templates: 820 H / lone pairs > check asl Checking 'asl'.... WARNING: The unperturbed charge of the unit: -75.000020 is not zero. Warning: Close contact of 1.068923 angstroms between .R.A and .R.A Warning: Close contact of 1.398372 angstroms between .R.A and .R.A Warning: Close contact of 1.430282 angstroms between .R.A and .R.A Warning: Close contact of 1.119720 angstroms between .R.A and .R.A Warning: Close contact of 1.468518 angstroms between .R.A and .R.A Checking parameters for unit 'asl'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 6 Unit is OK. > saveamberparm asl trna1.prmtop trna1.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -75.000020 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 516 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (no restraints) > solvatebox asl TIP3PBOX 10 Solute vdw bounding box: 61.090 51.636 78.616 Total bounding box for atom centers: 81.090 71.636 98.616 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 4 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 28.161524, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 28.161524, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 28.161524, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 28.161524, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 28.161524, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 37.548698, 28.161524, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 9.387175, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 9.387175, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 9.387175, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 9.387175, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 9.387175, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 37.548698, 9.387175, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, -9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, -9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, -9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, -9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, -9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 37.548698, -9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -28.161524, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -28.161524, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -28.161524, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -28.161524, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -28.161524, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 37.548698, -28.161524, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 28.161524, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 28.161524, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 28.161524, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 28.161524, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 28.161524, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 18.774349, 28.161524, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 9.387175, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 9.387175, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 9.387175, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 9.387175, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 9.387175, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 18.774349, 9.387175, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, -9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, -9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, -9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, -9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, -9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 18.774349, -9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -28.161524, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -28.161524, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -28.161524, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -28.161524, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -28.161524, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 18.774349, -28.161524, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 28.161524, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 28.161524, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 28.161524, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 28.161524, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 28.161524, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 0.000000, 28.161524, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 9.387175, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 9.387175, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 9.387175, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 9.387175, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 9.387175, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 0.000000, 9.387175, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, -9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, -9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, -9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, -9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, -9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 0.000000, -9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -28.161524, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -28.161524, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -28.161524, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -28.161524, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -28.161524, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 0.000000, -28.161524, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 28.161524, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 28.161524, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 28.161524, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 28.161524, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 28.161524, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -18.774349, 28.161524, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 9.387175, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 9.387175, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 9.387175, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 9.387175, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 9.387175, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -18.774349, 9.387175, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, -9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, -9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, -9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, -9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, -9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -18.774349, -9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -28.161524, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -28.161524, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -28.161524, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -28.161524, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -28.161524, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -18.774349, -28.161524, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 28.161524, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 28.161524, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 28.161524, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 28.161524, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 28.161524, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -37.548698, 28.161524, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 9.387175, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 9.387175, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 9.387175, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 9.387175, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 9.387175, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -37.548698, 9.387175, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, -9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, -9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, -9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, -9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, -9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -37.548698, -9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -28.161524, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -28.161524, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -28.161524, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -28.161524, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -28.161524, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -37.548698, -28.161524, -46.935873 Total vdw box size: 84.193 74.310 101.289 angstroms. Volume: 633707.545 A^3 Total mass 321708.556 amu, Density 0.843 g/cc Added 16500 residues. > addions asl Na+ 0 75 Na+ ions required to neutralize. Adding 75 counter ions to "asl" using 1A grid Total solute charge: -75.00 Max atom radius: 2.10 Grid extends from solute vdw + 7.91 to 14.01 Box: enclosing: -43.23 -37.87 -51.96 42.89 38.65 51.71 sized: 84.77 90.13 76.04 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 3 sec Volume = 3.97% of box, grid points 83231 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 13 sec (Replacing solvent molecule) Placed Na+ in asl at (9.07, 16.94, -0.20). (Replacing solvent molecule) Placed Na+ in asl at (19.56, -2.98, 20.08). (Replacing solvent molecule) Placed Na+ in asl at (-11.66, 1.45, 0.73). (Replacing solvent molecule) Placed Na+ in asl at (25.57, -0.10, -7.96). (Replacing solvent molecule) Placed Na+ in asl at (5.73, 21.09, -9.34). (Replacing solvent molecule) Placed Na+ in asl at (6.79, -18.88, 10.81). (Replacing solvent molecule) Placed Na+ in asl at (6.34, 22.85, 3.87). (Replacing solvent molecule) Placed Na+ in asl at (18.05, 13.52, -13.01). (Replacing solvent molecule) Placed Na+ in asl at (-16.29, -11.02, 17.40). (Replacing solvent molecule) Placed Na+ in asl at (17.13, -15.75, 1.03). (Replacing solvent molecule) Placed Na+ in asl at (-8.08, 4.00, -11.47). (Replacing solvent molecule) Placed Na+ in asl at (13.68, -0.28, 27.70). (Replacing solvent molecule) Placed Na+ in asl at (4.87, -22.47, -10.46). (Replacing solvent molecule) Placed Na+ in asl at (24.77, -4.45, 1.05). (Replacing solvent molecule) Placed Na+ in asl at (-12.19, -10.20, 1.79). (Replacing solvent molecule) Placed Na+ in asl at (17.11, -10.59, 16.96). (Replacing solvent molecule) Placed Na+ in asl at (-6.53, -14.18, -22.43). (Replacing solvent molecule) Placed Na+ in asl at (24.56, 13.77, 24.32). (Replacing solvent molecule) Placed Na+ in asl at (-4.68, 10.22, 33.85). (Replacing solvent molecule) Placed Na+ in asl at (26.37, -11.20, -6.61). (Replacing solvent molecule) Placed Na+ in asl at (-3.21, -19.64, 5.51). (Replacing solvent molecule) Placed Na+ in asl at (-2.79, 20.23, -0.83). (Replacing solvent molecule) Placed Na+ in asl at (0.30, -5.34, -34.55). (Replacing solvent molecule) Placed Na+ in asl at (10.11, 31.81, 13.53). (Replacing solvent molecule) Placed Na+ in asl at (5.39, 6.25, 34.07). (Replacing solvent molecule) Placed Na+ in asl at (-11.82, 15.20, 11.74). (Replacing solvent molecule) Placed Na+ in asl at (14.10, -8.55, -41.25). (Replacing solvent molecule) Placed Na+ in asl at (27.11, 5.38, -11.65). (Replacing solvent molecule) Placed Na+ in asl at (-18.47, -5.34, 3.00). (Replacing solvent molecule) Placed Na+ in asl at (3.94, 9.59, -23.94). (Replacing solvent molecule) Placed Na+ in asl at (-17.18, 2.89, 22.80). (Replacing solvent molecule) Placed Na+ in asl at (26.37, -11.20, -25.38). (Replacing solvent molecule) Placed Na+ in asl at (-11.17, -22.12, 23.29). (Replacing solvent molecule) Placed Na+ in asl at (18.83, 21.25, -2.29). (Replacing solvent molecule) Placed Na+ in asl at (13.62, -22.53, -8.16). (Replacing solvent molecule) Placed Na+ in asl at (27.25, -4.64, 15.74). (Replacing solvent molecule) Placed Na+ in asl at (6.79, 18.67, 29.58). (Replacing solvent molecule) Placed Na+ in asl at (-8.31, -9.22, -11.35). (Replacing solvent molecule) Placed Na+ in asl at (20.10, 6.15, -27.78). (Replacing solvent molecule) Placed Na+ in asl at (4.97, -10.08, 36.46). (Replacing solvent molecule) Placed Na+ in asl at (-5.15, 15.02, -8.16). (Replacing solvent molecule) Placed Na+ in asl at (-7.48, 20.69, 22.69). (Replacing solvent molecule) Placed Na+ in asl at (-16.03, -23.76, 36.83). (Replacing solvent molecule) Placed Na+ in asl at (-3.21, -19.64, -13.26). (Replacing solvent molecule) Placed Na+ in asl at (31.71, 13.39, 0.88). (Replacing solvent molecule) Placed Na+ in asl at (10.55, 18.35, -16.95). (Replacing solvent molecule) Placed Na+ in asl at (21.96, -24.79, -29.19). (Replacing solvent molecule) Placed Na+ in asl at (25.11, 4.07, 22.65). (Replacing solvent molecule) Placed Na+ in asl at (8.26, -19.21, 23.95). (Replacing solvent molecule) Placed Na+ in asl at (22.31, 28.97, 21.19). (Replacing solvent molecule) Placed Na+ in asl at (8.48, -4.64, -40.58). (Replacing solvent molecule) Placed Na+ in asl at (-11.17, -3.35, 42.06). (Replacing solvent molecule) Placed Na+ in asl at (-5.13, -7.79, -27.13). (Replacing solvent molecule) Placed Na+ in asl at (-16.03, -4.99, 18.06). (Replacing solvent molecule) Placed Na+ in asl at (-3.17, 30.55, 12.01). (Replacing solvent molecule) Placed Na+ in asl at (16.92, -16.07, 10.43). (Replacing solvent molecule) Placed Na+ in asl at (22.95, -20.03, -39.65). (Replacing solvent molecule) Placed Na+ in asl at (31.53, 17.40, 14.25). (Replacing solvent molecule) Placed Na+ in asl at (-13.34, 9.23, 26.35). (Replacing solvent molecule) Placed Na+ in asl at (25.01, -19.53, -11.79). (Replacing solvent molecule) Placed Na+ in asl at (-1.32, -25.97, 35.36). (Replacing solvent molecule) Placed Na+ in asl at (-13.34, 9.23, 7.58). (Replacing solvent molecule) Placed Na+ in asl at (14.10, 10.22, 33.85). (Replacing solvent molecule) Placed Na+ in asl at (22.79, -3.14, -35.25). (Replacing solvent molecule) Placed Na+ in asl at (-3.66, 6.98, -18.72). (Replacing solvent molecule) Placed Na+ in asl at (-16.44, -15.70, 44.28). (Replacing solvent molecule) Placed Na+ in asl at (10.47, 28.33, 26.20). (Replacing solvent molecule) Placed Na+ in asl at (-0.74, -26.24, -23.90). (Replacing solvent molecule) Placed Na+ in asl at (-8.67, -24.52, 13.53). (Replacing solvent molecule) Placed Na+ in asl at (29.03, 2.62, -22.24). (Replacing solvent molecule) Placed Na+ in asl at (11.68, -28.41, -41.69). (Replacing solvent molecule) Placed Na+ in asl at (28.92, -2.60, 8.33). (Replacing solvent molecule) Placed Na+ in asl at (24.56, 32.55, 5.55). (Replacing solvent molecule) Placed Na+ in asl at (6.34, 4.07, -33.68). (Replacing solvent molecule) Placed Na+ in asl at (3.13, -11.48, 42.44). Done adding ions. > saveamberparm asl trna1.prmtop trna1.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 516 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected WAT 16425 ) (no restraints) > asl=loadpdb trna.pdb Loading PDB file: ./trna.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue G, term: Terminal/beginning, seq. number: 0 to: RG5. Mapped residue C, term: Nonterminal, seq. number: 1 to: RC. Mapped residue G, term: Nonterminal, seq. number: 2 to: RG. Mapped residue G, term: Nonterminal, seq. number: 3 to: RG. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue U, term: Nonterminal, seq. number: 5 to: RU. Mapped residue U, term: Nonterminal, seq. number: 6 to: RU. Mapped residue U, term: Nonterminal, seq. number: 7 to: RU. Mapped residue A, term: Nonterminal, seq. number: 8 to: RA. (Residue 9: 2MG, Nonterminal, was not found in name map.) Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue U, term: Nonterminal, seq. number: 11 to: RU. Mapped residue C, term: Nonterminal, seq. number: 12 to: RC. Mapped residue A, term: Nonterminal, seq. number: 13 to: RA. Mapped residue G, term: Nonterminal, seq. number: 14 to: RG. (Residue 15: DHU, Nonterminal, was not found in name map.) (Residue 16: DHU, Nonterminal, was not found in name map.) Mapped residue G, term: Nonterminal, seq. number: 17 to: RG. Mapped residue G, term: Nonterminal, seq. number: 18 to: RG. Mapped residue G, term: Nonterminal, seq. number: 19 to: RG. Mapped residue A, term: Nonterminal, seq. number: 20 to: RA. Mapped residue G, term: Nonterminal, seq. number: 21 to: RG. Mapped residue A, term: Nonterminal, seq. number: 22 to: RA. Mapped residue G, term: Nonterminal, seq. number: 23 to: RG. Mapped residue C, term: Nonterminal, seq. number: 24 to: RC. (Residue 25: DMG, Nonterminal, was not found in name map.) Mapped residue C, term: Nonterminal, seq. number: 26 to: RC. Mapped residue C, term: Nonterminal, seq. number: 27 to: RC. Mapped residue A, term: Nonterminal, seq. number: 28 to: RA. Mapped residue G, term: Nonterminal, seq. number: 29 to: RG. Mapped residue A, term: Nonterminal, seq. number: 30 to: RA. (Residue 31: MRC, Nonterminal, was not found in name map.) Mapped residue U, term: Nonterminal, seq. number: 32 to: RU. (Residue 33: MRG, Nonterminal, was not found in name map.) Mapped residue A, term: Nonterminal, seq. number: 34 to: RA. Mapped residue A, term: Nonterminal, seq. number: 35 to: RA. (Residue 36: WBG, Nonterminal, was not found in name map.) Mapped residue A, term: Nonterminal, seq. number: 37 to: RA. (Residue 38: PSU, Nonterminal, was not found in name map.) (Residue 39: 5MC, Nonterminal, was not found in name map.) Mapped residue U, term: Nonterminal, seq. number: 40 to: RU. Mapped residue G, term: Nonterminal, seq. number: 41 to: RG. Mapped residue G, term: Nonterminal, seq. number: 42 to: RG. Mapped residue A, term: Nonterminal, seq. number: 43 to: RA. Mapped residue G, term: Nonterminal, seq. number: 44 to: RG. (Residue 45: 7MG, Nonterminal, was not found in name map.) Mapped residue U, term: Nonterminal, seq. number: 46 to: RU. Mapped residue C, term: Nonterminal, seq. number: 47 to: RC. (Residue 48: 5MC, Nonterminal, was not found in name map.) Mapped residue U, term: Nonterminal, seq. number: 49 to: RU. Mapped residue G, term: Nonterminal, seq. number: 50 to: RG. Mapped residue U, term: Nonterminal, seq. number: 51 to: RU. Mapped residue G, term: Nonterminal, seq. number: 52 to: RG. (Residue 53: 5MU, Nonterminal, was not found in name map.) (Residue 54: PSU, Nonterminal, was not found in name map.) Mapped residue C, term: Nonterminal, seq. number: 55 to: RC. Mapped residue G, term: Nonterminal, seq. number: 56 to: RG. (Residue 57: 1MA, Nonterminal, was not found in name map.) Mapped residue U, term: Nonterminal, seq. number: 58 to: RU. Mapped residue C, term: Nonterminal, seq. number: 59 to: RC. Mapped residue C, term: Nonterminal, seq. number: 60 to: RC. Mapped residue A, term: Nonterminal, seq. number: 61 to: RA. Mapped residue C, term: Nonterminal, seq. number: 62 to: RC. Mapped residue A, term: Nonterminal, seq. number: 63 to: RA. Mapped residue G, term: Nonterminal, seq. number: 64 to: RG. Mapped residue A, term: Nonterminal, seq. number: 65 to: RA. Mapped residue A, term: Nonterminal, seq. number: 66 to: RA. Mapped residue U, term: Nonterminal, seq. number: 67 to: RU. Mapped residue U, term: Nonterminal, seq. number: 68 to: RU. Mapped residue C, term: Nonterminal, seq. number: 69 to: RC. Mapped residue G, term: Nonterminal, seq. number: 70 to: RG. Mapped residue C, term: Nonterminal, seq. number: 71 to: RC. Mapped residue A, term: Nonterminal, seq. number: 72 to: RA. Mapped residue C, term: Nonterminal, seq. number: 73 to: RC. Mapped residue C, term: Nonterminal, seq. number: 74 to: RC. Mapped residue A, term: Terminal/last, seq. number: 75 to: RA3. Joining RG5 - RC Joining RC - RG Joining RG - RG Joining RG - RA Joining RA - RU Joining RU - RU Joining RU - RU Joining RU - RA Joining RA - 2MG Joining 2MG - RC Joining RC - RU Joining RU - RC Joining RC - RA Joining RA - RG Joining RG - DHU Joining DHU - DHU Joining DHU - RG Joining RG - RG Joining RG - RG Joining RG - RA Joining RA - RG Joining RG - RA Joining RA - RG Joining RG - RC Joining RC - DMG Joining DMG - RC Joining RC - RC Joining RC - RA Joining RA - RG Joining RG - RA Joining RA - MRC Joining MRC - RU Joining RU - MRG Joining MRG - RA Joining RA - RA Joining RA - WBG Joining WBG - RA Joining RA - PSU Joining PSU - 5MC Joining 5MC - RU Joining RU - RG Joining RG - RG Joining RG - RA Joining RA - RG Joining RG - 7MG Joining 7MG - RU Joining RU - RC Joining RC - 5MC Joining 5MC - RU Joining RU - RG Joining RG - RU Joining RU - RG Joining RG - 5MU Joining 5MU - PSU Joining PSU - RC Joining RC - RG Joining RG - 1MA Joining 1MA - RU Joining RU - RC Joining RC - RC Joining RC - RA Joining RA - RC Joining RC - RA Joining RA - RG Joining RG - RA Joining RA - RA Joining RA - RU Joining RU - RU Joining RU - RC Joining RC - RG Joining RG - RC Joining RC - RA Joining RA - RC Joining RC - RC Joining RC - RA3 total atoms in file: 1648 Leap added 862 missing atoms according to residue templates: 862 H / lone pairs > check asl Checking 'asl'.... WARNING: The unperturbed charge of the unit: -73.000180 is not zero. Warning: Close contact of 1.068923 angstroms between .R.A and .R.A Warning: Close contact of 1.398372 angstroms between .R.A and .R.A Warning: Close contact of 1.430282 angstroms between .R.A and .R.A Warning: Close contact of 1.127276 angstroms between .R.A and .R.A Checking parameters for unit 'asl'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 5 Unit is OK. > solvatebox asl TIP3PBOX 10 Solute vdw bounding box: 61.090 51.862 79.048 Total bounding box for atom centers: 81.090 71.862 99.048 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 4 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 28.161524, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 28.161524, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 28.161524, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 28.161524, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 28.161524, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 37.548698, 28.161524, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 9.387175, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 9.387175, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 9.387175, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 9.387175, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 9.387175, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 37.548698, 9.387175, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, -9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, -9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, -9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, -9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, -9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 37.548698, -9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -28.161524, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -28.161524, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -28.161524, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -28.161524, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -28.161524, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 37.548698, -28.161524, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 28.161524, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 28.161524, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 28.161524, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 28.161524, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 28.161524, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 18.774349, 28.161524, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 9.387175, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 9.387175, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 9.387175, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 9.387175, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 9.387175, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 18.774349, 9.387175, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, -9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, -9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, -9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, -9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, -9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 18.774349, -9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -28.161524, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -28.161524, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -28.161524, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -28.161524, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -28.161524, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 18.774349, -28.161524, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 28.161524, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 28.161524, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 28.161524, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 28.161524, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 28.161524, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 0.000000, 28.161524, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 9.387175, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 9.387175, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 9.387175, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 9.387175, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 9.387175, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 0.000000, 9.387175, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, -9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, -9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, -9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, -9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, -9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 0.000000, -9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -28.161524, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -28.161524, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -28.161524, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -28.161524, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -28.161524, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 0.000000, -28.161524, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 28.161524, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 28.161524, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 28.161524, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 28.161524, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 28.161524, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -18.774349, 28.161524, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 9.387175, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 9.387175, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 9.387175, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 9.387175, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 9.387175, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -18.774349, 9.387175, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, -9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, -9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, -9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, -9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, -9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -18.774349, -9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -28.161524, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -28.161524, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -28.161524, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -28.161524, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -28.161524, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -18.774349, -28.161524, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 28.161524, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 28.161524, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 28.161524, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 28.161524, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 28.161524, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -37.548698, 28.161524, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 9.387175, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 9.387175, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 9.387175, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 9.387175, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 9.387175, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -37.548698, 9.387175, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, -9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, -9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, -9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, -9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, -9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -37.548698, -9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -28.161524, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -28.161524, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -28.161524, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -28.161524, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -28.161524, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -37.548698, -28.161524, -46.935873 Total vdw box size: 84.193 75.097 102.444 angstroms. Volume: 647722.018 A^3 Total mass 324836.510 amu, Density 0.833 g/cc Added 16654 residues. > addions asl Na+ 0 73 Na+ ions required to neutralize. Adding 73 counter ions to "asl" using 1A grid Total solute charge: -73.00 Max atom radius: 2.10 Grid extends from solute vdw + 7.84 to 13.94 Box: enclosing: -43.16 -38.48 -51.94 42.82 38.29 52.02 sized: 84.84 89.52 76.06 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 4 sec Volume = 3.99% of box, grid points 83693 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 18 sec (Replacing solvent molecule) Placed Na+ in asl at (6.59, 17.63, -0.61). (Replacing solvent molecule) Placed Na+ in asl at (19.56, -3.37, 20.24). (Replacing solvent molecule) Placed Na+ in asl at (-11.66, 1.06, 0.89). (Replacing solvent molecule) Placed Na+ in asl at (25.57, -0.50, -7.80). (Replacing solvent molecule) Placed Na+ in asl at (14.86, -15.31, 16.16). (Replacing solvent molecule) Placed Na+ in asl at (18.05, 13.12, -12.84). (Replacing solvent molecule) Placed Na+ in asl at (-1.06, -17.84, 8.33). (Replacing solvent molecule) Placed Na+ in asl at (6.91, 25.13, 4.75). (Replacing solvent molecule) Placed Na+ in asl at (-16.29, -11.42, 17.56). (Replacing solvent molecule) Placed Na+ in asl at (13.67, -16.73, 2.62). (Replacing solvent molecule) Placed Na+ in asl at (-7.48, 1.52, -14.70). (Replacing solvent molecule) Placed Na+ in asl at (13.68, -0.67, 27.86). (Replacing solvent molecule) Placed Na+ in asl at (26.37, -11.60, -6.44). (Replacing solvent molecule) Placed Na+ in asl at (6.79, 18.28, -7.80). (Replacing solvent molecule) Placed Na+ in asl at (1.10, -20.58, -10.67). (Replacing solvent molecule) Placed Na+ in asl at (-4.40, 6.50, 34.86). (Replacing solvent molecule) Placed Na+ in asl at (-9.09, -12.40, 3.53). (Replacing solvent molecule) Placed Na+ in asl at (-6.53, -14.57, -22.27). (Replacing solvent molecule) Placed Na+ in asl at (28.88, -6.24, 2.87). (Replacing solvent molecule) Placed Na+ in asl at (0.30, -5.73, -34.39). (Replacing solvent molecule) Placed Na+ in asl at (24.14, 10.57, 24.34). (Replacing solvent molecule) Placed Na+ in asl at (-12.64, 11.10, 10.04). (Replacing solvent molecule) Placed Na+ in asl at (5.39, 5.86, 34.24). (Replacing solvent molecule) Placed Na+ in asl at (11.68, -6.76, -40.47). (Replacing solvent molecule) Placed Na+ in asl at (-18.47, -5.73, 3.16). (Replacing solvent molecule) Placed Na+ in asl at (16.62, -21.93, -5.88). (Replacing solvent molecule) Placed Na+ in asl at (11.68, 30.79, 15.85). (Replacing solvent molecule) Placed Na+ in asl at (-5.15, 14.62, -8.00). (Replacing solvent molecule) Placed Na+ in asl at (27.11, 4.99, -11.49). (Replacing solvent molecule) Placed Na+ in asl at (-17.18, 2.50, 22.96). (Replacing solvent molecule) Placed Na+ in asl at (11.88, 6.05, -26.91). (Replacing solvent molecule) Placed Na+ in asl at (6.68, -17.85, 13.74). (Replacing solvent molecule) Placed Na+ in asl at (26.37, -11.60, -25.22). (Replacing solvent molecule) Placed Na+ in asl at (-11.71, -21.05, 21.11). (Replacing solvent molecule) Placed Na+ in asl at (5.73, 20.69, 28.37). (Replacing solvent molecule) Placed Na+ in asl at (18.83, 20.85, -2.13). (Replacing solvent molecule) Placed Na+ in asl at (27.25, -5.03, 15.90). (Replacing solvent molecule) Placed Na+ in asl at (-5.11, 20.82, 2.62). (Replacing solvent molecule) Placed Na+ in asl at (4.97, -10.47, 36.62). (Replacing solvent molecule) Placed Na+ in asl at (-8.31, -9.61, -11.18). (Replacing solvent molecule) Placed Na+ in asl at (-8.22, 17.95, 20.76). (Replacing solvent molecule) Placed Na+ in asl at (-12.78, -23.62, 38.76). (Replacing solvent molecule) Placed Na+ in asl at (24.50, 1.92, -27.95). (Replacing solvent molecule) Placed Na+ in asl at (1.60, 8.65, -22.35). (Replacing solvent molecule) Placed Na+ in asl at (25.68, -12.42, 4.75). (Replacing solvent molecule) Placed Na+ in asl at (22.95, -20.43, -39.49). (Replacing solvent molecule) Placed Na+ in asl at (25.48, 19.48, 22.35). (Replacing solvent molecule) Placed Na+ in asl at (31.71, 12.99, 1.04). (Replacing solvent molecule) Placed Na+ in asl at (-12.64, 11.10, 28.82). (Replacing solvent molecule) Placed Na+ in asl at (-5.13, -8.19, -26.97). (Replacing solvent molecule) Placed Na+ in asl at (-16.81, -6.92, 43.04). (Replacing solvent molecule) Placed Na+ in asl at (6.96, -22.74, -6.87). (Replacing solvent molecule) Placed Na+ in asl at (-1.42, -27.42, 24.32). (Replacing solvent molecule) Placed Na+ in asl at (-6.90, 6.05, -8.13). (Replacing solvent molecule) Placed Na+ in asl at (15.99, 16.59, 28.92). (Replacing solvent molecule) Placed Na+ in asl at (9.40, -32.28, -24.11). (Replacing solvent molecule) Placed Na+ in asl at (-3.15, 26.68, 13.65). (Replacing solvent molecule) Placed Na+ in asl at (14.67, -11.88, 25.23). (Replacing solvent molecule) Placed Na+ in asl at (18.71, -11.40, -42.87). (Replacing solvent molecule) Placed Na+ in asl at (-17.00, -7.22, 20.15). (Replacing solvent molecule) Placed Na+ in asl at (26.61, 28.73, 12.04). (Replacing solvent molecule) Placed Na+ in asl at (24.77, -23.62, -17.56). (Replacing solvent molecule) Placed Na+ in asl at (6.71, 19.48, -15.20). (Replacing solvent molecule) Placed Na+ in asl at (12.28, 16.38, -14.76). (Replacing solvent molecule) Placed Na+ in asl at (-4.73, -4.33, 40.45). (Replacing solvent molecule) Placed Na+ in asl at (11.68, -28.81, -41.52). (Replacing solvent molecule) Placed Na+ in asl at (-0.24, -23.06, 36.64). (Replacing solvent molecule) Placed Na+ in asl at (28.00, 2.82, 0.52). (Replacing solvent molecule) Placed Na+ in asl at (11.31, 0.89, -43.20). (Replacing solvent molecule) Placed Na+ in asl at (-3.96, -24.20, -23.56). (Replacing solvent molecule) Placed Na+ in asl at (-23.92, -22.93, 29.55). (Replacing solvent molecule) Placed Na+ in asl at (14.15, 30.88, 23.02). (Replacing solvent molecule) Placed Na+ in asl at (9.22, 2.82, 38.07). Done adding ions. > saveamberparm asl wtrna.prmtop wtrna.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. ** No torsion terms for CB-N*-CR-H5 Building improper torsion parameters. ** Warning: No sp2 improper torsion term for CA-CT-N2-CT atoms are: C2 C10 N2 C11 ** Warning: No sp2 improper torsion term for CM-CA-N2-CT atoms are: C6 C2 N1 C10 total 521 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Parameter file was not saved. > edit 5MC > edit 7MG > asl=loadpdb trna2.pdb Loading PDB file: ./trna2.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue G, term: Terminal/beginning, seq. number: 0 to: RG5. Mapped residue C, term: Nonterminal, seq. number: 1 to: RC. Mapped residue G, term: Nonterminal, seq. number: 2 to: RG. Mapped residue G, term: Nonterminal, seq. number: 3 to: RG. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue U, term: Nonterminal, seq. number: 5 to: RU. Mapped residue U, term: Nonterminal, seq. number: 6 to: RU. Mapped residue U, term: Nonterminal, seq. number: 7 to: RU. Mapped residue A, term: Nonterminal, seq. number: 8 to: RA. (Residue 9: 2MG, Nonterminal, was not found in name map.) Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue U, term: Nonterminal, seq. number: 11 to: RU. Mapped residue C, term: Nonterminal, seq. number: 12 to: RC. Mapped residue A, term: Nonterminal, seq. number: 13 to: RA. Mapped residue G, term: Nonterminal, seq. number: 14 to: RG. (Residue 15: DHU, Nonterminal, was not found in name map.) (Residue 16: DHU, Nonterminal, was not found in name map.) Mapped residue G, term: Nonterminal, seq. number: 17 to: RG. Mapped residue G, term: Nonterminal, seq. number: 18 to: RG. Mapped residue G, term: Nonterminal, seq. number: 19 to: RG. Mapped residue A, term: Nonterminal, seq. number: 20 to: RA. Mapped residue G, term: Nonterminal, seq. number: 21 to: RG. Mapped residue A, term: Nonterminal, seq. number: 22 to: RA. Mapped residue G, term: Nonterminal, seq. number: 23 to: RG. Mapped residue C, term: Nonterminal, seq. number: 24 to: RC. Mapped residue G, term: Nonterminal, seq. number: 25 to: RG. Mapped residue C, term: Nonterminal, seq. number: 26 to: RC. Mapped residue C, term: Nonterminal, seq. number: 27 to: RC. Mapped residue A, term: Nonterminal, seq. number: 28 to: RA. Mapped residue G, term: Nonterminal, seq. number: 29 to: RG. Mapped residue A, term: Nonterminal, seq. number: 30 to: RA. Mapped residue C, term: Nonterminal, seq. number: 31 to: RC. Mapped residue U, term: Nonterminal, seq. number: 32 to: RU. Mapped residue G, term: Nonterminal, seq. number: 33 to: RG. Mapped residue A, term: Nonterminal, seq. number: 34 to: RA. Mapped residue A, term: Nonterminal, seq. number: 35 to: RA. Mapped residue G, term: Nonterminal, seq. number: 36 to: RG. Mapped residue A, term: Nonterminal, seq. number: 37 to: RA. (Residue 38: PSU, Nonterminal, was not found in name map.) (Residue 39: 5MC, Nonterminal, was not found in name map.) Mapped residue U, term: Nonterminal, seq. number: 40 to: RU. Mapped residue G, term: Nonterminal, seq. number: 41 to: RG. Mapped residue G, term: Nonterminal, seq. number: 42 to: RG. Mapped residue A, term: Nonterminal, seq. number: 43 to: RA. Mapped residue G, term: Nonterminal, seq. number: 44 to: RG. (Residue 45: 7MG, Nonterminal, was not found in name map.) Mapped residue U, term: Nonterminal, seq. number: 46 to: RU. Mapped residue C, term: Nonterminal, seq. number: 47 to: RC. Mapped residue C, term: Nonterminal, seq. number: 48 to: RC. Mapped residue U, term: Nonterminal, seq. number: 49 to: RU. Mapped residue G, term: Nonterminal, seq. number: 50 to: RG. Mapped residue U, term: Nonterminal, seq. number: 51 to: RU. Mapped residue G, term: Nonterminal, seq. number: 52 to: RG. Mapped residue U, term: Nonterminal, seq. number: 53 to: RU. (Residue 54: PSU, Nonterminal, was not found in name map.) Mapped residue C, term: Nonterminal, seq. number: 55 to: RC. Mapped residue G, term: Nonterminal, seq. number: 56 to: RG. Mapped residue A, term: Nonterminal, seq. number: 57 to: RA. Mapped residue U, term: Nonterminal, seq. number: 58 to: RU. Mapped residue C, term: Nonterminal, seq. number: 59 to: RC. Mapped residue C, term: Nonterminal, seq. number: 60 to: RC. Mapped residue A, term: Nonterminal, seq. number: 61 to: RA. Mapped residue C, term: Nonterminal, seq. number: 62 to: RC. Mapped residue A, term: Nonterminal, seq. number: 63 to: RA. Mapped residue G, term: Nonterminal, seq. number: 64 to: RG. Mapped residue A, term: Nonterminal, seq. number: 65 to: RA. Mapped residue A, term: Nonterminal, seq. number: 66 to: RA. Mapped residue U, term: Nonterminal, seq. number: 67 to: RU. Mapped residue U, term: Nonterminal, seq. number: 68 to: RU. Mapped residue C, term: Nonterminal, seq. number: 69 to: RC. Mapped residue G, term: Nonterminal, seq. number: 70 to: RG. Mapped residue C, term: Nonterminal, seq. number: 71 to: RC. Mapped residue A, term: Nonterminal, seq. number: 72 to: RA. Mapped residue C, term: Nonterminal, seq. number: 73 to: RC. Mapped residue C, term: Nonterminal, seq. number: 74 to: RC. Mapped residue A, term: Terminal/last, seq. number: 75 to: RA3. Joining RG5 - RC Joining RC - RG Joining RG - RG Joining RG - RA Joining RA - RU Joining RU - RU Joining RU - RU Joining RU - RA Joining RA - 2MG Joining 2MG - RC Joining RC - RU Joining RU - RC Joining RC - RA Joining RA - RG Joining RG - DHU Joining DHU - DHU Joining DHU - RG Joining RG - RG Joining RG - RG Joining RG - RA Joining RA - RG Joining RG - RA Joining RA - RG Joining RG - RC Joining RC - RG Joining RG - RC Joining RC - RC Joining RC - RA Joining RA - RG Joining RG - RA Joining RA - RC Joining RC - RU Joining RU - RG Joining RG - RA Joining RA - RA Joining RA - RG Joining RG - RA Joining RA - PSU Joining PSU - 5MC Joining 5MC - RU Joining RU - RG Joining RG - RG Joining RG - RA Joining RA - RG Joining RG - 7MG Joining 7MG - RU Joining RU - RC Joining RC - RC Joining RC - RU Joining RU - RG Joining RG - RU Joining RU - RG Joining RG - RU Joining RU - PSU Joining PSU - RC Joining RC - RG Joining RG - RA Joining RA - RU Joining RU - RC Joining RC - RC Joining RC - RA Joining RA - RC Joining RC - RA Joining RA - RG Joining RG - RA Joining RA - RA Joining RA - RU Joining RU - RU Joining RU - RC Joining RC - RG Joining RG - RC Joining RC - RA Joining RA - RC Joining RC - RC Joining RC - RA3 total atoms in file: 1637 Leap added 820 missing atoms according to residue templates: 820 H / lone pairs > check asl Checking 'asl'.... WARNING: The unperturbed charge of the unit: -74.000030 is not zero. Warning: Close contact of 1.068923 angstroms between .R.A and .R.A Warning: Close contact of 1.398372 angstroms between .R.A and .R.A Warning: Close contact of 1.430282 angstroms between .R.A and .R.A Warning: Close contact of 1.119720 angstroms between .R.A and .R.A Warning: Close contact of 1.468518 angstroms between .R.A and .R.A Warning: Close contact of 1.342671 angstroms between .R<5MC 40>.A and .R<5MC 40>.A Warning: Close contact of 1.342139 angstroms between .R<5MC 40>.A and .R<5MC 40>.A Checking parameters for unit 'asl'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 8 Unit is OK. > solvatebox asl TIP3PBOX 10 Solute vdw bounding box: 61.090 51.636 78.616 Total bounding box for atom centers: 81.090 71.636 98.616 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 4 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 28.161524, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 28.161524, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 28.161524, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 28.161524, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 28.161524, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 37.548698, 28.161524, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 9.387175, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 9.387175, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 9.387175, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 9.387175, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 9.387175, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 37.548698, 9.387175, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, -9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, -9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, -9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, -9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, -9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 37.548698, -9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -28.161524, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -28.161524, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -28.161524, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -28.161524, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -28.161524, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 37.548698, -28.161524, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 28.161524, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 28.161524, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 28.161524, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 28.161524, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 28.161524, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 18.774349, 28.161524, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 9.387175, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 9.387175, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 9.387175, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 9.387175, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 9.387175, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 18.774349, 9.387175, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, -9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, -9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, -9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, -9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, -9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 18.774349, -9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -28.161524, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -28.161524, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -28.161524, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -28.161524, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -28.161524, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 18.774349, -28.161524, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 28.161524, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 28.161524, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 28.161524, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 28.161524, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 28.161524, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 0.000000, 28.161524, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 9.387175, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 9.387175, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 9.387175, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 9.387175, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 9.387175, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 0.000000, 9.387175, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, -9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, -9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, -9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, -9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, -9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 0.000000, -9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -28.161524, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -28.161524, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -28.161524, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -28.161524, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -28.161524, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 0.000000, -28.161524, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 28.161524, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 28.161524, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 28.161524, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 28.161524, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 28.161524, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -18.774349, 28.161524, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 9.387175, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 9.387175, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 9.387175, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 9.387175, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 9.387175, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -18.774349, 9.387175, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, -9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, -9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, -9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, -9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, -9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -18.774349, -9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -28.161524, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -28.161524, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -28.161524, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -28.161524, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -28.161524, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -18.774349, -28.161524, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 28.161524, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 28.161524, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 28.161524, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 28.161524, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 28.161524, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -37.548698, 28.161524, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 9.387175, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 9.387175, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 9.387175, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 9.387175, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 9.387175, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -37.548698, 9.387175, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, -9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, -9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, -9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, -9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, -9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -37.548698, -9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -28.161524, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -28.161524, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -28.161524, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -28.161524, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -28.161524, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -37.548698, -28.161524, -46.935873 Total vdw box size: 84.193 74.310 101.289 angstroms. Volume: 633707.545 A^3 Total mass 321737.616 amu, Density 0.843 g/cc Added 16500 residues. > addions asl Na+ 0 74 Na+ ions required to neutralize. Adding 74 counter ions to "asl" using 1A grid Total solute charge: -74.00 Max atom radius: 2.10 Grid extends from solute vdw + 7.88 to 13.98 Box: enclosing: -43.19 -37.83 -51.92 42.85 38.61 51.68 sized: 84.81 90.17 76.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 4 sec Volume = 3.96% of box, grid points 83006 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 18 sec (Replacing solvent molecule) Placed Na+ in asl at (9.07, 16.94, -0.20). (Replacing solvent molecule) Placed Na+ in asl at (18.53, -3.89, 17.70). (Replacing solvent molecule) Placed Na+ in asl at (-11.66, 1.45, 0.73). (Replacing solvent molecule) Placed Na+ in asl at (25.57, -0.10, -7.96). (Replacing solvent molecule) Placed Na+ in asl at (6.68, -17.45, 13.58). (Replacing solvent molecule) Placed Na+ in asl at (6.34, 22.85, 3.87). (Replacing solvent molecule) Placed Na+ in asl at (20.74, 12.25, -13.44). (Replacing solvent molecule) Placed Na+ in asl at (-16.29, -11.02, 17.40). (Replacing solvent molecule) Placed Na+ in asl at (17.13, -15.75, 1.03). (Replacing solvent molecule) Placed Na+ in asl at (13.68, -0.28, 27.70). (Replacing solvent molecule) Placed Na+ in asl at (-8.08, 4.00, -11.47). (Replacing solvent molecule) Placed Na+ in asl at (5.73, 21.09, -9.34). (Replacing solvent molecule) Placed Na+ in asl at (4.87, -22.47, -10.46). (Replacing solvent molecule) Placed Na+ in asl at (26.37, -11.20, -6.61). (Replacing solvent molecule) Placed Na+ in asl at (-12.19, -10.20, 1.79). (Replacing solvent molecule) Placed Na+ in asl at (-1.66, 8.18, 35.73). (Replacing solvent molecule) Placed Na+ in asl at (24.56, 13.77, 24.32). (Replacing solvent molecule) Placed Na+ in asl at (-6.53, -14.18, -22.43). (Replacing solvent molecule) Placed Na+ in asl at (14.86, -14.92, 16.00). (Replacing solvent molecule) Placed Na+ in asl at (-3.21, -19.64, 5.51). (Replacing solvent molecule) Placed Na+ in asl at (-2.79, 20.23, -0.83). (Replacing solvent molecule) Placed Na+ in asl at (0.30, -5.34, -34.55). (Replacing solvent molecule) Placed Na+ in asl at (10.11, 31.81, 13.53). (Replacing solvent molecule) Placed Na+ in asl at (27.97, -6.89, 8.04). (Replacing solvent molecule) Placed Na+ in asl at (-11.82, 15.20, 11.74). (Replacing solvent molecule) Placed Na+ in asl at (14.10, -8.55, -41.25). (Replacing solvent molecule) Placed Na+ in asl at (-19.55, 1.78, 22.22). (Replacing solvent molecule) Placed Na+ in asl at (22.59, 1.79, 21.36). (Replacing solvent molecule) Placed Na+ in asl at (14.42, 6.70, -26.09). (Replacing solvent molecule) Placed Na+ in asl at (10.25, 2.62, 34.09). (Replacing solvent molecule) Placed Na+ in asl at (-18.47, -5.34, 3.00). (Replacing solvent molecule) Placed Na+ in asl at (26.37, -11.20, -25.38). (Replacing solvent molecule) Placed Na+ in asl at (18.83, 21.25, -2.29). (Replacing solvent molecule) Placed Na+ in asl at (-10.93, 10.35, 30.65). (Replacing solvent molecule) Placed Na+ in asl at (-11.17, -22.12, 23.29). (Replacing solvent molecule) Placed Na+ in asl at (13.62, -22.53, -8.16). (Replacing solvent molecule) Placed Na+ in asl at (-0.07, 7.77, -24.26). (Replacing solvent molecule) Placed Na+ in asl at (5.73, 21.09, 28.21). (Replacing solvent molecule) Placed Na+ in asl at (-4.74, -14.93, -6.93). (Replacing solvent molecule) Placed Na+ in asl at (29.83, 6.85, -2.90). (Replacing solvent molecule) Placed Na+ in asl at (-12.78, -23.23, 38.60). (Replacing solvent molecule) Placed Na+ in asl at (-5.15, 15.02, -8.16). (Replacing solvent molecule) Placed Na+ in asl at (23.65, -22.47, -29.23). (Replacing solvent molecule) Placed Na+ in asl at (8.41, -13.74, 28.64). (Replacing solvent molecule) Placed Na+ in asl at (24.60, -5.47, -1.63). (Replacing solvent molecule) Placed Na+ in asl at (-7.48, 20.69, 22.69). (Replacing solvent molecule) Placed Na+ in asl at (24.50, 2.31, -28.11). (Replacing solvent molecule) Placed Na+ in asl at (20.55, 30.72, 19.99). (Replacing solvent molecule) Placed Na+ in asl at (-5.13, -7.79, -27.13). (Replacing solvent molecule) Placed Na+ in asl at (-6.49, -2.00, 41.40). (Replacing solvent molecule) Placed Na+ in asl at (31.53, 17.40, 14.25). (Replacing solvent molecule) Placed Na+ in asl at (-3.21, -19.64, -13.26). (Replacing solvent molecule) Placed Na+ in asl at (8.48, -4.64, -40.58). (Replacing solvent molecule) Placed Na+ in asl at (15.99, 16.98, 28.76). (Replacing solvent molecule) Placed Na+ in asl at (10.67, 18.08, -12.37). (Replacing solvent molecule) Placed Na+ in asl at (9.07, -20.60, 18.58). (Replacing solvent molecule) Placed Na+ in asl at (-13.34, 9.23, 7.58). (Replacing solvent molecule) Placed Na+ in asl at (21.11, -19.71, -42.01). (Replacing solvent molecule) Placed Na+ in asl at (-3.17, 30.55, 12.01). (Replacing solvent molecule) Placed Na+ in asl at (-0.78, -16.99, 41.00). (Replacing solvent molecule) Placed Na+ in asl at (-11.98, -18.88, 10.81). (Replacing solvent molecule) Placed Na+ in asl at (25.01, -19.53, -11.79). (Replacing solvent molecule) Placed Na+ in asl at (-17.99, -2.98, 38.85). (Replacing solvent molecule) Placed Na+ in asl at (27.11, 5.38, -11.65). (Replacing solvent molecule) Placed Na+ in asl at (5.34, -31.96, -28.07). (Replacing solvent molecule) Placed Na+ in asl at (-8.21, -4.21, -13.98). (Replacing solvent molecule) Placed Na+ in asl at (29.33, 18.35, 1.83). (Replacing solvent molecule) Placed Na+ in asl at (-21.69, -16.60, 43.06). (Replacing solvent molecule) Placed Na+ in asl at (10.67, -19.47, 6.41). (Replacing solvent molecule) Placed Na+ in asl at (-24.62, -5.39, 19.65). (Replacing solvent molecule) Placed Na+ in asl at (10.11, -24.52, -42.79). (Replacing solvent molecule) Placed Na+ in asl at (33.13, 2.13, 13.83). (Replacing solvent molecule) Placed Na+ in asl at (6.34, 4.07, -33.68). (Replacing solvent molecule) Placed Na+ in asl at (-1.42, -27.03, 24.15). Done adding ions. > charge asl Total unperturbed charge: -0.000030 Total perturbed charge: -0.000030 > saveamberparm asl trna2.prmtop trna2.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. ** No torsion terms for CB-N*-CR-H5 Building improper torsion parameters. total 517 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Parameter file was not saved. > edit 5MC > edit 7MC Creating a new, empty UNIT "7MC" > edit 7MG > quit Quit log started: Thu Apr 28 11:53:41 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: /home/PraYagRaj/amber14/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: 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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> # >> # Define the PDB name map for the amino acids and 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 oldff/leaprc.ff99bsc0 ----- Source: /home/PraYagRaj/amber14/dat/leap/cmd/oldff/leaprc.ff99bsc0 ----- Source of /home/PraYagRaj/amber14/dat/leap/cmd/oldff/leaprc.ff99bsc0 done >> logFile leap.log log started: Thu Apr 28 11:53:56 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field >> # using parmbsc0 for nucleic acid. >> # ----- NOTE: this is designed for PDB format 3! >> # >> # 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" } >> { "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" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "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: /home/PraYagRaj/amber14/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: 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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/dat/leap/lib/DNA_CI.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 >> # >> # Load water and ions >> # >> loadOff ions94.lib Loading library: /home/PraYagRaj/amber14/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: /home/PraYagRaj/amber14/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and 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" "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 "DG" "DG5" } { 1 "DG" "DG3" } >> { 0 "DA" "DA5" } { 1 "DA" "DA3" } >> { 0 "DC" "DC5" } { 1 "DC" "DC3" } >> { 0 "DT" "DT5" } { 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 -> RG5 for 0G -> RG5 Substituting map 1G -> RG3 for 1G -> RG3 Substituting map G -> RG for G -> RG Substituting map GN -> RGN for GN -> RGN Substituting map 0A -> RA5 for 0A -> RA5 Substituting map 1A -> RA3 for 1A -> RA3 Substituting map A -> RA for A -> RA Substituting map AN -> RAN for AN -> RAN Substituting map 0C -> RC5 for 0C -> RC5 Substituting map 1C -> RC3 for 1C -> RC3 Substituting map C -> RC for C -> RC Substituting map CN -> RCN for CN -> RCN Substituting map 0U -> RU5 for 0U -> RU5 Substituting map 1U -> RU3 for 1U -> RU3 Substituting map U -> RU for U -> RU Substituting map UN -> RUN for UN -> RUN >> >> 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" "H2'1" } >> { "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" } >> { "HO2'" "HO'2" } >> { "HO5'" "H5T" } >> { "HO3'" "H3T" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> { "OP1" "O1P" } >> { "OP2" "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 O2* -> O2' for O2* -> O2' 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 Substituting map HO2' -> HO'2 for HO2' -> HO'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 > > source leaprc.modrna08 ----- Source: /home/PraYagRaj/amber14/dat/leap/cmd/leaprc.modrna08 ----- Source of /home/PraYagRaj/amber14/dat/leap/cmd/leaprc.modrna08 done >> # >> # ----- leaprc for loading modified RNA nucleotides. The parameters are >> # described here: >> >> # R. Aduri, B.T. Psciuk, P. Saro, H. Taniga, >> # Schlegel, H.B. and J. SantaLucia, Jr. AMBER force field parameters >> # for the naturally occurring modified nucleosides in RNA. >> # J. Chem. Theory Comput. 3, 1465-1475, 2007. >> # >> # To use these residues, load this file into leap, after the Amber-FF, e.g.: >> # >> # > source leaprc.ff13SB >> # > source leaprc.modrna08 >> # >> >> modrna08 = loadAmberParams all_modrna08.frcmod Loading parameters: /home/PraYagRaj/amber14/dat/leap/parm/all_modrna08.frcmod Reading force field modification type file (frcmod) Reading title: parameters for the 107 modified nucleosides in RNA: see ../cmd/leaprc.modrna08 (UNKNOWN ATOM TYPE: CZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: SO) (UNKNOWN ATOM TYPE: SS) >> loadOff all_modrna08.lib Loading library: /home/PraYagRaj/amber14/dat/leap/lib/all_modrna08.lib Loading: 13P Loading: 1MA Loading: 1MG Loading: 1MI Loading: 1MP Loading: 26A Loading: 27G Loading: 2MA Loading: 2MG Loading: 2RG Loading: 2SC Loading: 2SU Loading: 3AU Loading: 3MC Loading: 3MP Loading: 3MU Loading: 4AC Loading: 4MC Loading: 4SU Loading: 52U Loading: 5AU Loading: 5CU Loading: 5DU Loading: 5FC Loading: 5HU Loading: 5MC Loading: 5MU Loading: 5TU Loading: 66A Loading: 6AA Loading: 6GA Loading: 6IA Loading: 6MA Loading: 6TA Loading: 7MG Loading: BCU Loading: BUG Loading: CMU Loading: DAG Loading: DHU Loading: DMA Loading: DMG Loading: DMU Loading: DWG Loading: EQG Loading: ESU Loading: HCU Loading: HIA Loading: HMC Loading: HNA Loading: HWG Loading: INO Loading: IWG Loading: K2C Loading: M1G Loading: M2A Loading: M3U Loading: M4C Loading: MAC Loading: MAU Loading: MCU Loading: MEU Loading: MFC Loading: MMA Loading: MMC Loading: MMG Loading: MMI Loading: MMU Loading: MRA Loading: MRC Loading: MRG Loading: MRI Loading: MRP Loading: MRU Loading: MSU Loading: MTA Loading: MTG Loading: N2G Loading: OAU Loading: OCU Loading: OEU Loading: OMU Loading: PBG Loading: PSU Loading: QGG Loading: QMG Loading: QUG Loading: SAU Loading: SCU Loading: SEU Loading: SIA Loading: SMA Loading: SMU Loading: SPA Loading: STA Loading: STU Loading: WBG Loading: WMG Loading: WYG > > asl=loadpdb trna3.pdb Loading PDB file: ./trna3.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue G, term: Terminal/beginning, seq. number: 0 to: RG5. Mapped residue C, term: Nonterminal, seq. number: 1 to: RC. Mapped residue G, term: Nonterminal, seq. number: 2 to: RG. Mapped residue G, term: Nonterminal, seq. number: 3 to: RG. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue U, term: Nonterminal, seq. number: 5 to: RU. Mapped residue U, term: Nonterminal, seq. number: 6 to: RU. Mapped residue U, term: Nonterminal, seq. number: 7 to: RU. Mapped residue A, term: Nonterminal, seq. number: 8 to: RA. Mapped residue G, term: Nonterminal, seq. number: 9 to: RG. Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue U, term: Nonterminal, seq. number: 11 to: RU. Mapped residue C, term: Nonterminal, seq. number: 12 to: RC. Mapped residue A, term: Nonterminal, seq. number: 13 to: RA. Mapped residue G, term: Nonterminal, seq. number: 14 to: RG. (Residue 15: DHU, Nonterminal, was not found in name map.) (Residue 16: DHU, Nonterminal, was not found in name map.) Mapped residue G, term: Nonterminal, seq. number: 17 to: RG. Mapped residue G, term: Nonterminal, seq. number: 18 to: RG. Mapped residue G, term: Nonterminal, seq. number: 19 to: RG. Mapped residue A, term: Nonterminal, seq. number: 20 to: RA. Mapped residue G, term: Nonterminal, seq. number: 21 to: RG. Mapped residue A, term: Nonterminal, seq. number: 22 to: RA. Mapped residue G, term: Nonterminal, seq. number: 23 to: RG. Mapped residue C, term: Nonterminal, seq. number: 24 to: RC. Mapped residue G, term: Nonterminal, seq. number: 25 to: RG. Mapped residue C, term: Nonterminal, seq. number: 26 to: RC. Mapped residue C, term: Nonterminal, seq. number: 27 to: RC. Mapped residue A, term: Nonterminal, seq. number: 28 to: RA. Mapped residue G, term: Nonterminal, seq. number: 29 to: RG. Mapped residue A, term: Nonterminal, seq. number: 30 to: RA. Mapped residue C, term: Nonterminal, seq. number: 31 to: RC. Mapped residue U, term: Nonterminal, seq. number: 32 to: RU. Mapped residue G, term: Nonterminal, seq. number: 33 to: RG. Mapped residue A, term: Nonterminal, seq. number: 34 to: RA. Mapped residue A, term: Nonterminal, seq. number: 35 to: RA. Mapped residue G, term: Nonterminal, seq. number: 36 to: RG. Mapped residue A, term: Nonterminal, seq. number: 37 to: RA. Mapped residue U, term: Nonterminal, seq. number: 38 to: RU. Mapped residue C, term: Nonterminal, seq. number: 39 to: RC. Mapped residue U, term: Nonterminal, seq. number: 40 to: RU. Mapped residue G, term: Nonterminal, seq. number: 41 to: RG. Mapped residue G, term: Nonterminal, seq. number: 42 to: RG. Mapped residue A, term: Nonterminal, seq. number: 43 to: RA. Mapped residue G, term: Nonterminal, seq. number: 44 to: RG. (Residue 45: 7MG, Nonterminal, was not found in name map.) Mapped residue U, term: Nonterminal, seq. number: 46 to: RU. Mapped residue C, term: Nonterminal, seq. number: 47 to: RC. Mapped residue C, term: Nonterminal, seq. number: 48 to: RC. Mapped residue U, term: Nonterminal, seq. number: 49 to: RU. Mapped residue G, term: Nonterminal, seq. number: 50 to: RG. Mapped residue U, term: Nonterminal, seq. number: 51 to: RU. Mapped residue G, term: Nonterminal, seq. number: 52 to: RG. Mapped residue U, term: Nonterminal, seq. number: 53 to: RU. Mapped residue U, term: Nonterminal, seq. number: 54 to: RU. Mapped residue C, term: Nonterminal, seq. number: 55 to: RC. Mapped residue G, term: Nonterminal, seq. number: 56 to: RG. Mapped residue A, term: Nonterminal, seq. number: 57 to: RA. Mapped residue U, term: Nonterminal, seq. number: 58 to: RU. Mapped residue C, term: Nonterminal, seq. number: 59 to: RC. Mapped residue C, term: Nonterminal, seq. number: 60 to: RC. Mapped residue A, term: Nonterminal, seq. number: 61 to: RA. Mapped residue C, term: Nonterminal, seq. number: 62 to: RC. Mapped residue A, term: Nonterminal, seq. number: 63 to: RA. Mapped residue G, term: Nonterminal, seq. number: 64 to: RG. Mapped residue A, term: Nonterminal, seq. number: 65 to: RA. Mapped residue A, term: Nonterminal, seq. number: 66 to: RA. Mapped residue U, term: Nonterminal, seq. number: 67 to: RU. Mapped residue U, term: Nonterminal, seq. number: 68 to: RU. Mapped residue C, term: Nonterminal, seq. number: 69 to: RC. Mapped residue G, term: Nonterminal, seq. number: 70 to: RG. Mapped residue C, term: Nonterminal, seq. number: 71 to: RC. Mapped residue A, term: Nonterminal, seq. number: 72 to: RA. Mapped residue C, term: Nonterminal, seq. number: 73 to: RC. Mapped residue C, term: Nonterminal, seq. number: 74 to: RC. Mapped residue A, term: Terminal/last, seq. number: 75 to: RA3. Joining RG5 - RC Joining RC - RG Joining RG - RG Joining RG - RA Joining RA - RU Joining RU - RU Joining RU - RU Joining RU - RA Joining RA - RG Joining RG - RC Joining RC - RU Joining RU - RC Joining RC - RA Joining RA - RG Joining RG - DHU Joining DHU - DHU Joining DHU - RG Joining RG - RG Joining RG - RG Joining RG - RA Joining RA - RG Joining RG - RA Joining RA - RG Joining RG - RC Joining RC - RG Joining RG - RC Joining RC - RC Joining RC - RA Joining RA - RG Joining RG - RA Joining RA - RC Joining RC - RU Joining RU - RG Joining RG - RA Joining RA - RA Joining RA - RG Joining RG - RA Joining RA - RU Joining RU - RC Joining RC - RU Joining RU - RG Joining RG - RG Joining RG - RA Joining RA - RG Joining RG - 7MG Joining 7MG - RU Joining RU - RC Joining RC - RC Joining RC - RU Joining RU - RG Joining RG - RU Joining RU - RG Joining RG - RU Joining RU - RU Joining RU - RC Joining RC - RG Joining RG - RA Joining RA - RU Joining RU - RC Joining RC - RC Joining RC - RA Joining RA - RC Joining RC - RA Joining RA - RG Joining RG - RA Joining RA - RA Joining RA - RU Joining RU - RU Joining RU - RC Joining RC - RG Joining RG - RC Joining RC - RA Joining RA - RC Joining RC - RC Joining RC - RA3 total atoms in file: 1633 Leap added 818 missing atoms according to residue templates: 818 H / lone pairs > check asl Checking 'asl'.... WARNING: The unperturbed charge of the unit: -74.000030 is not zero. Warning: Close contact of 1.068923 angstroms between .R.A and .R.A Warning: Close contact of 1.398372 angstroms between .R.A and .R.A Warning: Close contact of 1.430282 angstroms between .R.A and .R.A Warning: Close contact of 1.119720 angstroms between .R.A and .R.A Warning: Close contact of 1.468518 angstroms between .R.A and .R.A Checking parameters for unit 'asl'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 6 Unit is OK. > solvatebox asl TIP3PBOX 10 Solute vdw bounding box: 61.090 51.636 78.616 Total bounding box for atom centers: 81.090 71.636 98.616 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 5 y= 4 z= 6 Adding box at: x=0 y=0 z=0 Center of solvent box is: 37.548698, 28.161524, 46.935873 Adding box at: x=0 y=0 z=1 Center of solvent box is: 37.548698, 28.161524, 28.161524 Adding box at: x=0 y=0 z=2 Center of solvent box is: 37.548698, 28.161524, 9.387175 Adding box at: x=0 y=0 z=3 Center of solvent box is: 37.548698, 28.161524, -9.387175 Adding box at: x=0 y=0 z=4 Center of solvent box is: 37.548698, 28.161524, -28.161524 Adding box at: x=0 y=0 z=5 Center of solvent box is: 37.548698, 28.161524, -46.935873 Adding box at: x=0 y=1 z=0 Center of solvent box is: 37.548698, 9.387175, 46.935873 Adding box at: x=0 y=1 z=1 Center of solvent box is: 37.548698, 9.387175, 28.161524 Adding box at: x=0 y=1 z=2 Center of solvent box is: 37.548698, 9.387175, 9.387175 Adding box at: x=0 y=1 z=3 Center of solvent box is: 37.548698, 9.387175, -9.387175 Adding box at: x=0 y=1 z=4 Center of solvent box is: 37.548698, 9.387175, -28.161524 Adding box at: x=0 y=1 z=5 Center of solvent box is: 37.548698, 9.387175, -46.935873 Adding box at: x=0 y=2 z=0 Center of solvent box is: 37.548698, -9.387175, 46.935873 Adding box at: x=0 y=2 z=1 Center of solvent box is: 37.548698, -9.387175, 28.161524 Adding box at: x=0 y=2 z=2 Center of solvent box is: 37.548698, -9.387175, 9.387175 Adding box at: x=0 y=2 z=3 Center of solvent box is: 37.548698, -9.387175, -9.387175 Adding box at: x=0 y=2 z=4 Center of solvent box is: 37.548698, -9.387175, -28.161524 Adding box at: x=0 y=2 z=5 Center of solvent box is: 37.548698, -9.387175, -46.935873 Adding box at: x=0 y=3 z=0 Center of solvent box is: 37.548698, -28.161524, 46.935873 Adding box at: x=0 y=3 z=1 Center of solvent box is: 37.548698, -28.161524, 28.161524 Adding box at: x=0 y=3 z=2 Center of solvent box is: 37.548698, -28.161524, 9.387175 Adding box at: x=0 y=3 z=3 Center of solvent box is: 37.548698, -28.161524, -9.387175 Adding box at: x=0 y=3 z=4 Center of solvent box is: 37.548698, -28.161524, -28.161524 Adding box at: x=0 y=3 z=5 Center of solvent box is: 37.548698, -28.161524, -46.935873 Adding box at: x=1 y=0 z=0 Center of solvent box is: 18.774349, 28.161524, 46.935873 Adding box at: x=1 y=0 z=1 Center of solvent box is: 18.774349, 28.161524, 28.161524 Adding box at: x=1 y=0 z=2 Center of solvent box is: 18.774349, 28.161524, 9.387175 Adding box at: x=1 y=0 z=3 Center of solvent box is: 18.774349, 28.161524, -9.387175 Adding box at: x=1 y=0 z=4 Center of solvent box is: 18.774349, 28.161524, -28.161524 Adding box at: x=1 y=0 z=5 Center of solvent box is: 18.774349, 28.161524, -46.935873 Adding box at: x=1 y=1 z=0 Center of solvent box is: 18.774349, 9.387175, 46.935873 Adding box at: x=1 y=1 z=1 Center of solvent box is: 18.774349, 9.387175, 28.161524 Adding box at: x=1 y=1 z=2 Center of solvent box is: 18.774349, 9.387175, 9.387175 Adding box at: x=1 y=1 z=3 Center of solvent box is: 18.774349, 9.387175, -9.387175 Adding box at: x=1 y=1 z=4 Center of solvent box is: 18.774349, 9.387175, -28.161524 Adding box at: x=1 y=1 z=5 Center of solvent box is: 18.774349, 9.387175, -46.935873 Adding box at: x=1 y=2 z=0 Center of solvent box is: 18.774349, -9.387175, 46.935873 Adding box at: x=1 y=2 z=1 Center of solvent box is: 18.774349, -9.387175, 28.161524 Adding box at: x=1 y=2 z=2 Center of solvent box is: 18.774349, -9.387175, 9.387175 Adding box at: x=1 y=2 z=3 Center of solvent box is: 18.774349, -9.387175, -9.387175 Adding box at: x=1 y=2 z=4 Center of solvent box is: 18.774349, -9.387175, -28.161524 Adding box at: x=1 y=2 z=5 Center of solvent box is: 18.774349, -9.387175, -46.935873 Adding box at: x=1 y=3 z=0 Center of solvent box is: 18.774349, -28.161524, 46.935873 Adding box at: x=1 y=3 z=1 Center of solvent box is: 18.774349, -28.161524, 28.161524 Adding box at: x=1 y=3 z=2 Center of solvent box is: 18.774349, -28.161524, 9.387175 Adding box at: x=1 y=3 z=3 Center of solvent box is: 18.774349, -28.161524, -9.387175 Adding box at: x=1 y=3 z=4 Center of solvent box is: 18.774349, -28.161524, -28.161524 Adding box at: x=1 y=3 z=5 Center of solvent box is: 18.774349, -28.161524, -46.935873 Adding box at: x=2 y=0 z=0 Center of solvent box is: 0.000000, 28.161524, 46.935873 Adding box at: x=2 y=0 z=1 Center of solvent box is: 0.000000, 28.161524, 28.161524 Adding box at: x=2 y=0 z=2 Center of solvent box is: 0.000000, 28.161524, 9.387175 Adding box at: x=2 y=0 z=3 Center of solvent box is: 0.000000, 28.161524, -9.387175 Adding box at: x=2 y=0 z=4 Center of solvent box is: 0.000000, 28.161524, -28.161524 Adding box at: x=2 y=0 z=5 Center of solvent box is: 0.000000, 28.161524, -46.935873 Adding box at: x=2 y=1 z=0 Center of solvent box is: 0.000000, 9.387175, 46.935873 Adding box at: x=2 y=1 z=1 Center of solvent box is: 0.000000, 9.387175, 28.161524 Adding box at: x=2 y=1 z=2 Center of solvent box is: 0.000000, 9.387175, 9.387175 Adding box at: x=2 y=1 z=3 Center of solvent box is: 0.000000, 9.387175, -9.387175 Adding box at: x=2 y=1 z=4 Center of solvent box is: 0.000000, 9.387175, -28.161524 Adding box at: x=2 y=1 z=5 Center of solvent box is: 0.000000, 9.387175, -46.935873 Adding box at: x=2 y=2 z=0 Center of solvent box is: 0.000000, -9.387175, 46.935873 Adding box at: x=2 y=2 z=1 Center of solvent box is: 0.000000, -9.387175, 28.161524 Adding box at: x=2 y=2 z=2 Center of solvent box is: 0.000000, -9.387175, 9.387175 Adding box at: x=2 y=2 z=3 Center of solvent box is: 0.000000, -9.387175, -9.387175 Adding box at: x=2 y=2 z=4 Center of solvent box is: 0.000000, -9.387175, -28.161524 Adding box at: x=2 y=2 z=5 Center of solvent box is: 0.000000, -9.387175, -46.935873 Adding box at: x=2 y=3 z=0 Center of solvent box is: 0.000000, -28.161524, 46.935873 Adding box at: x=2 y=3 z=1 Center of solvent box is: 0.000000, -28.161524, 28.161524 Adding box at: x=2 y=3 z=2 Center of solvent box is: 0.000000, -28.161524, 9.387175 Adding box at: x=2 y=3 z=3 Center of solvent box is: 0.000000, -28.161524, -9.387175 Adding box at: x=2 y=3 z=4 Center of solvent box is: 0.000000, -28.161524, -28.161524 Adding box at: x=2 y=3 z=5 Center of solvent box is: 0.000000, -28.161524, -46.935873 Adding box at: x=3 y=0 z=0 Center of solvent box is: -18.774349, 28.161524, 46.935873 Adding box at: x=3 y=0 z=1 Center of solvent box is: -18.774349, 28.161524, 28.161524 Adding box at: x=3 y=0 z=2 Center of solvent box is: -18.774349, 28.161524, 9.387175 Adding box at: x=3 y=0 z=3 Center of solvent box is: -18.774349, 28.161524, -9.387175 Adding box at: x=3 y=0 z=4 Center of solvent box is: -18.774349, 28.161524, -28.161524 Adding box at: x=3 y=0 z=5 Center of solvent box is: -18.774349, 28.161524, -46.935873 Adding box at: x=3 y=1 z=0 Center of solvent box is: -18.774349, 9.387175, 46.935873 Adding box at: x=3 y=1 z=1 Center of solvent box is: -18.774349, 9.387175, 28.161524 Adding box at: x=3 y=1 z=2 Center of solvent box is: -18.774349, 9.387175, 9.387175 Adding box at: x=3 y=1 z=3 Center of solvent box is: -18.774349, 9.387175, -9.387175 Adding box at: x=3 y=1 z=4 Center of solvent box is: -18.774349, 9.387175, -28.161524 Adding box at: x=3 y=1 z=5 Center of solvent box is: -18.774349, 9.387175, -46.935873 Adding box at: x=3 y=2 z=0 Center of solvent box is: -18.774349, -9.387175, 46.935873 Adding box at: x=3 y=2 z=1 Center of solvent box is: -18.774349, -9.387175, 28.161524 Adding box at: x=3 y=2 z=2 Center of solvent box is: -18.774349, -9.387175, 9.387175 Adding box at: x=3 y=2 z=3 Center of solvent box is: -18.774349, -9.387175, -9.387175 Adding box at: x=3 y=2 z=4 Center of solvent box is: -18.774349, -9.387175, -28.161524 Adding box at: x=3 y=2 z=5 Center of solvent box is: -18.774349, -9.387175, -46.935873 Adding box at: x=3 y=3 z=0 Center of solvent box is: -18.774349, -28.161524, 46.935873 Adding box at: x=3 y=3 z=1 Center of solvent box is: -18.774349, -28.161524, 28.161524 Adding box at: x=3 y=3 z=2 Center of solvent box is: -18.774349, -28.161524, 9.387175 Adding box at: x=3 y=3 z=3 Center of solvent box is: -18.774349, -28.161524, -9.387175 Adding box at: x=3 y=3 z=4 Center of solvent box is: -18.774349, -28.161524, -28.161524 Adding box at: x=3 y=3 z=5 Center of solvent box is: -18.774349, -28.161524, -46.935873 Adding box at: x=4 y=0 z=0 Center of solvent box is: -37.548698, 28.161524, 46.935873 Adding box at: x=4 y=0 z=1 Center of solvent box is: -37.548698, 28.161524, 28.161524 Adding box at: x=4 y=0 z=2 Center of solvent box is: -37.548698, 28.161524, 9.387175 Adding box at: x=4 y=0 z=3 Center of solvent box is: -37.548698, 28.161524, -9.387175 Adding box at: x=4 y=0 z=4 Center of solvent box is: -37.548698, 28.161524, -28.161524 Adding box at: x=4 y=0 z=5 Center of solvent box is: -37.548698, 28.161524, -46.935873 Adding box at: x=4 y=1 z=0 Center of solvent box is: -37.548698, 9.387175, 46.935873 Adding box at: x=4 y=1 z=1 Center of solvent box is: -37.548698, 9.387175, 28.161524 Adding box at: x=4 y=1 z=2 Center of solvent box is: -37.548698, 9.387175, 9.387175 Adding box at: x=4 y=1 z=3 Center of solvent box is: -37.548698, 9.387175, -9.387175 Adding box at: x=4 y=1 z=4 Center of solvent box is: -37.548698, 9.387175, -28.161524 Adding box at: x=4 y=1 z=5 Center of solvent box is: -37.548698, 9.387175, -46.935873 Adding box at: x=4 y=2 z=0 Center of solvent box is: -37.548698, -9.387175, 46.935873 Adding box at: x=4 y=2 z=1 Center of solvent box is: -37.548698, -9.387175, 28.161524 Adding box at: x=4 y=2 z=2 Center of solvent box is: -37.548698, -9.387175, 9.387175 Adding box at: x=4 y=2 z=3 Center of solvent box is: -37.548698, -9.387175, -9.387175 Adding box at: x=4 y=2 z=4 Center of solvent box is: -37.548698, -9.387175, -28.161524 Adding box at: x=4 y=2 z=5 Center of solvent box is: -37.548698, -9.387175, -46.935873 Adding box at: x=4 y=3 z=0 Center of solvent box is: -37.548698, -28.161524, 46.935873 Adding box at: x=4 y=3 z=1 Center of solvent box is: -37.548698, -28.161524, 28.161524 Adding box at: x=4 y=3 z=2 Center of solvent box is: -37.548698, -28.161524, 9.387175 Adding box at: x=4 y=3 z=3 Center of solvent box is: -37.548698, -28.161524, -9.387175 Adding box at: x=4 y=3 z=4 Center of solvent box is: -37.548698, -28.161524, -28.161524 Adding box at: x=4 y=3 z=5 Center of solvent box is: -37.548698, -28.161524, -46.935873 Total vdw box size: 84.193 74.310 101.289 angstroms. Volume: 633707.545 A^3 Total mass 321727.580 amu, Density 0.843 g/cc Added 16501 residues. > addions asl Na+ 0 74 Na+ ions required to neutralize. Adding 74 counter ions to "asl" using 1A grid Total solute charge: -74.00 Max atom radius: 2.10 Grid extends from solute vdw + 7.88 to 13.98 Box: enclosing: -43.19 -37.83 -51.92 42.85 38.61 51.68 sized: 84.81 90.17 76.08 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 grid build: 3 sec Volume = 3.96% of box, grid points 82978 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 13 sec (Replacing solvent molecule) Placed Na+ in asl at (9.07, 16.94, -0.20). (Replacing solvent molecule) Placed Na+ in asl at (18.53, -3.89, 17.70). (Replacing solvent molecule) Placed Na+ in asl at (-11.66, 1.45, 0.73). (Replacing solvent molecule) Placed Na+ in asl at (25.57, -0.10, -7.96). (Replacing solvent molecule) Placed Na+ in asl at (6.68, -17.45, 13.58). (Replacing solvent molecule) Placed Na+ in asl at (6.34, 22.85, 3.87). (Replacing solvent molecule) Placed Na+ in asl at (20.74, 12.25, -13.44). (Replacing solvent molecule) Placed Na+ in asl at (-16.29, -11.02, 17.40). (Replacing solvent molecule) Placed Na+ in asl at (17.13, -15.75, 1.03). (Replacing solvent molecule) Placed Na+ in asl at (13.68, -0.28, 27.70). (Replacing solvent molecule) Placed Na+ in asl at (-8.08, 4.00, -11.47). (Replacing solvent molecule) Placed Na+ in asl at (5.73, 21.09, -9.34). (Replacing solvent molecule) Placed Na+ in asl at (4.87, -22.47, -10.46). (Replacing solvent molecule) Placed Na+ in asl at (26.37, -11.20, -6.61). (Replacing solvent molecule) Placed Na+ in asl at (-12.19, -10.20, 1.79). (Replacing solvent molecule) Placed Na+ in asl at (24.56, 13.77, 24.32). (Replacing solvent molecule) Placed Na+ in asl at (-1.66, 8.18, 35.73). (Replacing solvent molecule) Placed Na+ in asl at (-6.53, -14.18, -22.43). (Replacing solvent molecule) Placed Na+ in asl at (14.86, -14.92, 16.00). (Replacing solvent molecule) Placed Na+ in asl at (-3.21, -19.64, 5.51). (Replacing solvent molecule) Placed Na+ in asl at (10.11, 31.81, 13.53). (Replacing solvent molecule) Placed Na+ in asl at (0.30, -5.34, -34.55). (Replacing solvent molecule) Placed Na+ in asl at (-2.79, 20.23, -0.83). (Replacing solvent molecule) Placed Na+ in asl at (27.97, -6.89, 8.04). (Replacing solvent molecule) Placed Na+ in asl at (-11.82, 15.20, 11.74). (Replacing solvent molecule) Placed Na+ in asl at (14.10, -8.55, -41.25). (Replacing solvent molecule) Placed Na+ in asl at (-19.55, 1.78, 22.22). (Replacing solvent molecule) Placed Na+ in asl at (22.59, 1.79, 21.36). (Replacing solvent molecule) Placed Na+ in asl at (14.42, 6.70, -26.09). (Replacing solvent molecule) Placed Na+ in asl at (10.25, 2.62, 34.09). (Replacing solvent molecule) Placed Na+ in asl at (-18.47, -5.34, 3.00). (Replacing solvent molecule) Placed Na+ in asl at (18.83, 21.25, -2.29). (Replacing solvent molecule) Placed Na+ in asl at (26.37, -11.20, -25.38). (Replacing solvent molecule) Placed Na+ in asl at (-10.93, 10.35, 30.65). (Replacing solvent molecule) Placed Na+ in asl at (-11.17, -22.12, 23.29). (Replacing solvent molecule) Placed Na+ in asl at (13.62, -22.53, -8.16). (Replacing solvent molecule) Placed Na+ in asl at (-0.07, 7.77, -24.26). (Replacing solvent molecule) Placed Na+ in asl at (5.73, 21.09, 28.21). (Replacing solvent molecule) Placed Na+ in asl at (-4.74, -14.93, -6.93). (Replacing solvent molecule) Placed Na+ in asl at (29.83, 6.85, -2.90). (Replacing solvent molecule) Placed Na+ in asl at (-12.78, -23.23, 38.60). (Replacing solvent molecule) Placed Na+ in asl at (-5.15, 15.02, -8.16). (Replacing solvent molecule) Placed Na+ in asl at (8.41, -13.74, 28.64). (Replacing solvent molecule) Placed Na+ in asl at (23.65, -22.47, -29.23). (Replacing solvent molecule) Placed Na+ in asl at (24.60, -5.47, -1.63). (Replacing solvent molecule) Placed Na+ in asl at (-7.48, 20.69, 22.69). (Replacing solvent molecule) Placed Na+ in asl at (20.55, 30.72, 19.99). (Replacing solvent molecule) Placed Na+ in asl at (24.50, 2.31, -28.11). (Replacing solvent molecule) Placed Na+ in asl at (-5.13, -7.79, -27.13). (Replacing solvent molecule) Placed Na+ in asl at (-6.49, -2.00, 41.40). (Replacing solvent molecule) Placed Na+ in asl at (31.53, 17.40, 14.25). (Replacing solvent molecule) Placed Na+ in asl at (-3.21, -19.64, -13.26). (Replacing solvent molecule) Placed Na+ in asl at (8.48, -4.64, -40.58). (Replacing solvent molecule) Placed Na+ in asl at (15.99, 16.98, 28.76). (Replacing solvent molecule) Placed Na+ in asl at (9.07, -20.60, 18.58). (Replacing solvent molecule) Placed Na+ in asl at (10.67, 18.08, -12.37). (Replacing solvent molecule) Placed Na+ in asl at (-13.34, 9.23, 7.58). (Replacing solvent molecule) Placed Na+ in asl at (21.11, -19.71, -42.01). (Replacing solvent molecule) Placed Na+ in asl at (-3.17, 30.55, 12.01). (Replacing solvent molecule) Placed Na+ in asl at (-0.78, -16.99, 41.00). (Replacing solvent molecule) Placed Na+ in asl at (25.01, -19.53, -11.79). (Replacing solvent molecule) Placed Na+ in asl at (-11.98, -18.88, 10.81). (Replacing solvent molecule) Placed Na+ in asl at (-17.99, -2.98, 38.85). (Replacing solvent molecule) Placed Na+ in asl at (27.11, 5.38, -11.65). (Replacing solvent molecule) Placed Na+ in asl at (5.34, -31.96, -28.07). (Replacing solvent molecule) Placed Na+ in asl at (-8.21, -4.21, -13.98). (Replacing solvent molecule) Placed Na+ in asl at (29.33, 18.35, 1.83). (Replacing solvent molecule) Placed Na+ in asl at (-21.69, -16.60, 43.06). (Replacing solvent molecule) Placed Na+ in asl at (10.67, -19.47, 6.41). (Replacing solvent molecule) Placed Na+ in asl at (-24.62, -5.39, 19.65). (Replacing solvent molecule) Placed Na+ in asl at (33.13, 2.13, 13.83). (Replacing solvent molecule) Placed Na+ in asl at (10.11, -24.52, -42.79). (Replacing solvent molecule) Placed Na+ in asl at (6.34, 4.07, -33.68). (Replacing solvent molecule) Placed Na+ in asl at (3.54, 28.97, 21.19). Done adding ions. > saveamberparm asl trna3.prmtop trna3.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. ** No torsion terms for CB-N*-CR-H5 Building improper torsion parameters. total 517 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Parameter file was not saved. > quit Quit