Log file: ./leap.log >> # >> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> { "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: /u/local/apps/amber/current/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) >> frcmod99SB = loadamberparams frcmod.ff99SB Loading parameters: /u/local/apps/amber/current/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /u/local/apps/amber/current/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: /u/local/apps/amber/current/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: /u/local/apps/amber/current/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: /u/local/apps/amber/current/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 water and ions >> # >> loadOff ions94.lib Loading library: /u/local/apps/amber/current/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: /u/local/apps/amber/current/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> >> # >> # assumed that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > njw = loadpdb "/u/home/campus/template/3NJW.pdb" Loading PDB file: /u/home/campus/template/3NJW.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. Mapped residue GLY, term: Terminal/beginning, seq. number: 0 to: NGLY. (Residue 1: LEU, Nonterminal, was not found in name map.) (Residue 2: PRO, Nonterminal, was not found in name map.) (Residue 3: TRP, Nonterminal, was not found in name map.) (Residue 4: GLY, Nonterminal, was not found in name map.) (Residue 5: CYX, Nonterminal, was not found in name map.) (Residue 6: PRO, Nonterminal, was not found in name map.) (Residue 7: SER, Nonterminal, was not found in name map.) (Residue 8: ASP, Nonterminal, was not found in name map.) (Residue 9: ILE, Nonterminal, was not found in name map.) (Residue 10: PRO, Nonterminal, was not found in name map.) (Residue 11: GLY, Nonterminal, was not found in name map.) (Residue 12: TRP, Nonterminal, was not found in name map.) (Residue 13: ASN, Nonterminal, was not found in name map.) (Residue 14: THR, Nonterminal, was not found in name map.) (Residue 15: PRO, Nonterminal, was not found in name map.) (Residue 16: TRP, Nonterminal, was not found in name map.) (Residue 17: ALA, Nonterminal, was not found in name map.) Mapped residue CYX, term: Terminal/last, seq. number: 18 to: CCYX. (Residue 19: HOH, Terminal/beginning, was not found in name map.) (Residue 20: HOH, Nonterminal, was not found in name map.) (Residue 21: HOH, Nonterminal, was not found in name map.) (Residue 22: HOH, Nonterminal, was not found in name map.) (Residue 23: HOH, Nonterminal, was not found in name map.) (Residue 24: HOH, Nonterminal, was not found in name map.) (Residue 25: HOH, Nonterminal, was not found in name map.) (Residue 26: HOH, Nonterminal, was not found in name map.) (Residue 27: HOH, Nonterminal, was not found in name map.) (Residue 28: HOH, Nonterminal, was not found in name map.) (Residue 29: HOH, Nonterminal, was not found in name map.) (Residue 30: HOH, Nonterminal, was not found in name map.) (Residue 31: HOH, Nonterminal, was not found in name map.) (Residue 32: HOH, Nonterminal, was not found in name map.) (Residue 33: HOH, Nonterminal, was not found in name map.) (Residue 34: HOH, Nonterminal, was not found in name map.) (Residue 35: HOH, Nonterminal, was not found in name map.) (Residue 36: HOH, Nonterminal, was not found in name map.) (Residue 37: HOH, Nonterminal, was not found in name map.) (Residue 38: HOH, Nonterminal, was not found in name map.) (Residue 39: HOH, Nonterminal, was not found in name map.) (Residue 40: HOH, Nonterminal, was not found in name map.) (Residue 41: HOH, Nonterminal, was not found in name map.) (Residue 42: HOH, Nonterminal, was not found in name map.) (Residue 43: HOH, Terminal/last, was not found in name map.) Joining NGLY - LEU Joining LEU - PRO Joining PRO - TRP Joining TRP - GLY Joining GLY - CYX Joining CYX - PRO Joining PRO - SER Joining SER - ASP Added missing heavy atom: .R.A Joining ASP - ILE Joining ILE - PRO Joining PRO - GLY Joining GLY - TRP Joining TRP - ASN Joining ASN - THR Joining THR - PRO Joining PRO - TRP Joining TRP - ALA Joining ALA - CCYX Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 Starting new chain with TP3 total atoms in file: 169 Leap added 177 missing atoms according to residue templates: 1 Heavy 176 H / lone pairs > solvatebox njw TIP3PBOX 8.0 Solute vdw bounding box: 23.835 20.015 22.193 Total bounding box for atom centers: 39.835 36.015 38.193 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 3 y= 2 z= 3 Adding box at: x=0 y=0 z=0 Center of solvent box is: 18.774349, 9.387175, 18.774349 Adding box at: x=0 y=0 z=1 Center of solvent box is: 18.774349, 9.387175, 0.000000 Adding box at: x=0 y=0 z=2 Center of solvent box is: 18.774349, 9.387175, -18.774349 Adding box at: x=0 y=1 z=0 Center of solvent box is: 18.774349, -9.387175, 18.774349 Adding box at: x=0 y=1 z=1 Center of solvent box is: 18.774349, -9.387175, 0.000000 Adding box at: x=0 y=1 z=2 Center of solvent box is: 18.774349, -9.387175, -18.774349 Adding box at: x=1 y=0 z=0 Center of solvent box is: 0.000000, 9.387175, 18.774349 Adding box at: x=1 y=0 z=1 Center of solvent box is: 0.000000, 9.387175, 0.000000 Adding box at: x=1 y=0 z=2 Center of solvent box is: 0.000000, 9.387175, -18.774349 Adding box at: x=1 y=1 z=0 Center of solvent box is: 0.000000, -9.387175, 18.774349 Adding box at: x=1 y=1 z=1 Center of solvent box is: 0.000000, -9.387175, 0.000000 Adding box at: x=1 y=1 z=2 Center of solvent box is: 0.000000, -9.387175, -18.774349 Adding box at: x=2 y=0 z=0 Center of solvent box is: -18.774349, 9.387175, 18.774349 Adding box at: x=2 y=0 z=1 Center of solvent box is: -18.774349, 9.387175, 0.000000 Adding box at: x=2 y=0 z=2 Center of solvent box is: -18.774349, 9.387175, -18.774349 Adding box at: x=2 y=1 z=0 Center of solvent box is: -18.774349, -9.387175, 18.774349 Adding box at: x=2 y=1 z=1 Center of solvent box is: -18.774349, -9.387175, 0.000000 Adding box at: x=2 y=1 z=2 Center of solvent box is: -18.774349, -9.387175, -18.774349 Total vdw box size: 42.812 39.115 41.374 angstroms. Volume: 69286.805 A^3 Total mass 28880.132 amu, Density 0.692 g/cc Added 1464 residues. > saveamberparm njw njw.prmtop njw.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -1.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Could not find bond parameter for: N3 - C Building angle parameters. Could not find angle parameter: CT - N3 - C Could not find angle parameter: H - N3 - C Could not find angle parameter: H - N3 - C Could not find angle parameter: H - N3 - C Could not find angle parameter: N3 - C - CT Could not find angle parameter: N3 - C - O2 Could not find angle parameter: N3 - C - O2 Building proper torsion parameters. ** No torsion terms for CT-N3-C-CT ** No torsion terms for CT-N3-C-O2 ** No torsion terms for CT-N3-C-O2 ** No torsion terms for H-N3-C-CT ** No torsion terms for H-N3-C-O2 ** No torsion terms for H-N3-C-O2 ** No torsion terms for H-N3-C-CT ** No torsion terms for H-N3-C-O2 ** No torsion terms for H-N3-C-O2 ** No torsion terms for H-N3-C-CT ** No torsion terms for H-N3-C-O2 ** No torsion terms for H-N3-C-O2 Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for CT-O2-C-N3 atoms are: CB OD1 CG N ** Warning: No sp2 improper torsion term for CT-O2-C-N3 atoms are: CB OD2 CG N ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 62 improper torsions applied Building H-Bond parameters. Parameter file was not saved.