log started: Tue May 15 15:12:49 2012 Log file: ./leap.log > # > # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field > # ----- this file is updated 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" "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: /lap/amber/11.0.17_AT1.5/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: /lap/amber/11.0.17_AT1.5/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: /lap/amber/11.0.17_AT1.5/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: /lap/amber/11.0.17_AT1.5/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: /lap/amber/11.0.17_AT1.5/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: /lap/amber/11.0.17_AT1.5/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: /lap/amber/11.0.17_AT1.5/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: /lap/amber/11.0.17_AT1.5/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" "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" } > > } > > addPdbAtomMap { > { "O5*" "O5'" } > { "C5*" "C5'" } > { "C4*" "C4'" } > { "O4*" "O4'" } > { "C3*" "C3'" } > { "O3*" "O3'" } > { "C2*" "C2'" } > { "C1*" "C1'" } > { "C5M" "C7" } > { "O2*" "O2'" } > { "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" } > { "O1'" "O4'" } > { "OA" "O1P" } > { "OB" "O2P" } > { "OP1" "O1P" } > { "OP2" "O2P" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > glycam = loadamberparams parm99.dat Loading parameters: /lap/amber/11.0.17_AT1.5/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) > MGR = loadmol2 MGR.mol2 Loading Mol2 file: ./MGR.mol2 Reading MOLECULE named MGR > set MGR name "MGR" > set MGR head MGR.1.N > set MGR tail MGR.1.C > set MGR.1 connect0 MGR.1.N > set MGR.1 connect1 MGR.1.C > LYA = loadmol2 LYA.mol2 Loading Mol2 file: ./LYA.mol2 Reading MOLECULE named LYA > set LYA name "LYA" > set LYA head LYA.1.N > set LYA tail LYA.1.C > set LYA.1 connect0 LYA.1.N > set LYA.1 connect1 LYA.1.C > x = loadpdb pep1_H.pdb Loading PDB file: ./pep1_H.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: ILE, Nonterminal, was not found in name map.) (Residue 2: ALA, Nonterminal, was not found in name map.) (Residue 3: GLY, Nonterminal, was not found in name map.) (Residue 4: PHE, Nonterminal, was not found in name map.) (Residue 5: MGR, Nonterminal, was not found in name map.) (Residue 6: GLY, Nonterminal, was not found in name map.) (Residue 7: GLU, Nonterminal, was not found in name map.) (Residue 8: GLN, Nonterminal, was not found in name map.) (Residue 9: GLY, Nonterminal, was not found in name map.) (Residue 10: PRO, Nonterminal, was not found in name map.) (Residue 11: LYA, Terminal/last, was not found in name map.) Joining NGLY - ILE Joining ILE - ALA Joining ALA - GLY Joining GLY - PHE Joining PHE - MGR Joining MGR - GLY Joining GLY - GLU Joining GLU - GLN Joining GLN - GLY Joining GLY - PRO Joining PRO - LYA total atoms in file: 192 > check x Checking 'x'.... WARNING: The unperturbed charge of the unit: 1.999800 is not zero. Warning: Close contact of 1.321006 angstroms between .R.A and .R.A Checking parameters for unit 'x'. Checking for bond parameters. Could not find bond parameter for: CG - H1 Could not find bond parameter for: CG - OH Could not find bond parameter for: CG - H1 Could not find bond parameter for: CG - OH Could not find bond parameter for: CG - CG Could not find bond parameter for: CG - H1 Could not find bond parameter for: CG - OH Could not find bond parameter for: CG - CG Could not find bond parameter for: CG - H1 Could not find bond parameter for: CG - H1 Could not find bond parameter for: CG - OH Could not find bond parameter for: CG - H1 Could not find bond parameter for: CG - CG Could not find bond parameter for: CG - CG Could not find bond parameter for: OS - CG Could not find bond parameter for: CG - H2 Could not find bond parameter for: CG - OS Could not find bond parameter for: CG - CG Could not find bond parameter for: OS - CG Could not find bond parameter for: C - H Checking for angle parameters. Could not find angle parameter: H1 - CG - OH Could not find angle parameter: CG - OH - HO Could not find angle parameter: OH - CG - CG Could not find angle parameter: H1 - CG - OH Could not find angle parameter: H1 - CG - CG Could not find angle parameter: CG - OH - HO Could not find angle parameter: CG - CG - H1 Could not find angle parameter: CG - CG - OH Could not find angle parameter: OH - CG - CG Could not find angle parameter: H1 - CG - OH Could not find angle parameter: H1 - CG - CG Could not find angle parameter: CG - OH - HO Could not find angle parameter: CG - CG - H1 Could not find angle parameter: CG - CG - OH Could not find angle parameter: CG - CG - CG Could not find angle parameter: H1 - CG - OH Could not find angle parameter: H1 - CG - H1 Could not find angle parameter: H1 - CG - OH Could not find angle parameter: CG - CG - CG Could not find angle parameter: CG - OH - HO Could not find angle parameter: H1 - CG - CG Could not find angle parameter: H1 - CG - CG Could not find angle parameter: CG - CG - H1 Could not find angle parameter: CG - CG - H1 Could not find angle parameter: CG - CG - OH Could not find angle parameter: CG - CG - H1 Could not find angle parameter: CG - CG - OH Could not find angle parameter: CG - CG - CG Could not find angle parameter: OS - CG - CG Could not find angle parameter: OS - CG - H1 Could not find angle parameter: OS - CG - CG Could not find angle parameter: OS - CG - CG Could not find angle parameter: H2 - CG - OS Could not find angle parameter: H2 - CG - CG Could not find angle parameter: CG - OS - CG Could not find angle parameter: CG - CG - CG Could not find angle parameter: CG - CG - H1 Could not find angle parameter: CG - CG - OH Could not find angle parameter: OS - CG - H2 Could not find angle parameter: OS - CG - OS Could not find angle parameter: OS - CG - CG Could not find angle parameter: CT - OS - CG Could not find angle parameter: O - C - H Could not find angle parameter: CT - C - H There are missing parameters. check: Warnings: 2 Unit is OK. > quit Quit