log started: Wed Jun 23 21:04:34 2010 Log file: ./leap.log >> # >> # ----- leaprc for loading the parm99 additive force field, no lone pairs >> # assumes that any unspecified nucleic acids are DNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> { "EP" "" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm99 = loadamberparams parm99.dat Loading parameters: /home/mdatt/amber9/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 (UNKNOWN ATOM TYPE: HZ) (UNKNOWN ATOM TYPE: NY) (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: LP) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /home/mdatt/amber9/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/mdatt/amber9/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/mdatt/amber9/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/mdatt/amber9/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 ions94.lib Loading library: /home/mdatt/amber9/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/mdatt/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> 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 > > mol1 = loadpdb oligo.pdb Loading PDB file: ./oligo.pdb Enter zPdbReadScan from call depth 0. Warning: name change in pdb file residue 19 ; this residue is split into DA and D. Warning: name change in pdb file residue 19 ; this residue is split into D and DA. 2 residues had naming warnings. There are split residues; residue sequence numbers will not correspond to those in the pdb. -- residue 19: duplicate [ H5'] atoms (total 2) ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE: (same-name atoms are reduced to a single atom) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: DG, Terminal/beginning, was not found in name map.) (Residue 1: DG, Nonterminal, was not found in name map.) (Residue 2: DT, Nonterminal, was not found in name map.) (Residue 3: DT, Nonterminal, was not found in name map.) (Residue 4: DT, Nonterminal, was not found in name map.) (Residue 5: DA, Nonterminal, was not found in name map.) (Residue 6: DT, Nonterminal, was not found in name map.) (Residue 7: DT, Nonterminal, was not found in name map.) (Residue 8: DA, Nonterminal, was not found in name map.) (Residue 9: DA, Nonterminal, was not found in name map.) (Residue 10: DC, Nonterminal, was not found in name map.) (Residue 11: DT, Nonterminal, was not found in name map.) (Residue 12: DG, Nonterminal, was not found in name map.) (Residue 13: DT, Nonterminal, was not found in name map.) (Residue 14: DT, Nonterminal, was not found in name map.) (Residue 15: DT, Nonterminal, was not found in name map.) (Residue 16: DA, Nonterminal, was not found in name map.) (Residue 17: DT, Terminal/last, was not found in name map.) (Residue 18: DA, Terminal/beginning, was not found in name map.) (Residue 19: D, Nonterminal, was not found in name map.) Unknown residue: D number: 19 type: Nonterminal (Residue 20: DA, Nonterminal, was not found in name map.) (Residue 21: DT, Nonterminal, was not found in name map.) (Residue 22: DA, Nonterminal, was not found in name map.) (Residue 23: DA, Nonterminal, was not found in name map.) (Residue 24: DA, Nonterminal, was not found in name map.) (Residue 25: DC, Nonterminal, was not found in name map.) (Residue 26: DA, Nonterminal, was not found in name map.) (Residue 27: DG, Nonterminal, was not found in name map.) (Residue 28: DT, Nonterminal, was not found in name map.) (Residue 29: DT, Nonterminal, was not found in name map.) (Residue 30: DA, Nonterminal, was not found in name map.) (Residue 31: DA, Nonterminal, was not found in name map.) (Residue 32: DT, Nonterminal, was not found in name map.) (Residue 33: DA, Nonterminal, was not found in name map.) (Residue 34: DA, Nonterminal, was not found in name map.) (Residue 35: DA, Nonterminal, was not found in name map.) (Residue 36: DC, Nonterminal, was not found in name map.) (Residue 37: DC, Terminal/last, was not found in name map.) Created a new atom named: H5T within residue: .R Created a new atom named: H2' within residue: .R Added missing heavy atom: .R.A

Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining DG - DG Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DG - DT Created a new atom named: H5' within residue: .R

Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DC Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DC - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DG Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DG - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H3T within residue: .R
Created a new atom named: H5T within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A

Added missing heavy atom: .R.A Added missing heavy atom: .R.A Creating new UNIT for residue: D sequence: 20 One sided connection. Residue: missing connect0 atom. Created a new atom named: H2' within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A

Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining DA - DT Created a new atom named: H5' within residue: .R

Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DC Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DC - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DG Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DG - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DC Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DC - DC Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3T within residue: .R total atoms in file: 1146 Leap added 112 missing atoms according to residue templates: 27 Heavy 85 H / lone pairs The file contained 77 atoms not in residue templates log started: Wed Jun 23 21:07:24 2010 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: /home/mdatt/amber9/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: /home/mdatt/amber9/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: /home/mdatt/amber9/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/mdatt/amber9/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/mdatt/amber9/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/mdatt/amber9/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: /home/mdatt/amber9/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/mdatt/amber9/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: T4E Loading: TIP3PBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TP3 Loading: TP4 Loading: TP5 >> 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 > > mol1 = loadpdb oligo.pdb Loading PDB file: ./oligo.pdb Enter zPdbReadScan from call depth 0. Warning: name change in pdb file residue 19 ; this residue is split into DA and D. Warning: name change in pdb file residue 19 ; this residue is split into D and DA. 2 residues had naming warnings. There are split residues; residue sequence numbers will not correspond to those in the pdb. -- residue 19: duplicate [ H5'] atoms (total 2) ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE: (same-name atoms are reduced to a single atom) Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: DG, Terminal/beginning, was not found in name map.) (Residue 1: DG, Nonterminal, was not found in name map.) (Residue 2: DT, Nonterminal, was not found in name map.) (Residue 3: DT, Nonterminal, was not found in name map.) (Residue 4: DT, Nonterminal, was not found in name map.) (Residue 5: DA, Nonterminal, was not found in name map.) (Residue 6: DT, Nonterminal, was not found in name map.) (Residue 7: DT, Nonterminal, was not found in name map.) (Residue 8: DA, Nonterminal, was not found in name map.) (Residue 9: DA, Nonterminal, was not found in name map.) (Residue 10: DC, Nonterminal, was not found in name map.) (Residue 11: DT, Nonterminal, was not found in name map.) (Residue 12: DG, Nonterminal, was not found in name map.) (Residue 13: DT, Nonterminal, was not found in name map.) (Residue 14: DT, Nonterminal, was not found in name map.) (Residue 15: DT, Nonterminal, was not found in name map.) (Residue 16: DA, Nonterminal, was not found in name map.) (Residue 17: DT, Terminal/last, was not found in name map.) (Residue 18: DA, Terminal/beginning, was not found in name map.) (Residue 19: D, Nonterminal, was not found in name map.) Unknown residue: D number: 19 type: Nonterminal (Residue 20: DA, Nonterminal, was not found in name map.) (Residue 21: DT, Nonterminal, was not found in name map.) (Residue 22: DA, Nonterminal, was not found in name map.) (Residue 23: DA, Nonterminal, was not found in name map.) (Residue 24: DA, Nonterminal, was not found in name map.) (Residue 25: DC, Nonterminal, was not found in name map.) (Residue 26: DA, Nonterminal, was not found in name map.) (Residue 27: DG, Nonterminal, was not found in name map.) (Residue 28: DT, Nonterminal, was not found in name map.) (Residue 29: DT, Nonterminal, was not found in name map.) (Residue 30: DA, Nonterminal, was not found in name map.) (Residue 31: DA, Nonterminal, was not found in name map.) (Residue 32: DT, Nonterminal, was not found in name map.) (Residue 33: DA, Nonterminal, was not found in name map.) (Residue 34: DA, Nonterminal, was not found in name map.) (Residue 35: DA, Nonterminal, was not found in name map.) (Residue 36: DC, Nonterminal, was not found in name map.) (Residue 37: DC, Terminal/last, was not found in name map.) Created a new atom named: H5T within residue: .R Created a new atom named: H2' within residue: .R Added missing heavy atom: .R.A

Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining DG - DG Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DG - DT Created a new atom named: H5' within residue: .R

Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DC Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DC - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DG Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DG - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H3T within residue: .R
Created a new atom named: H5T within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Added missing heavy atom: .R.A Added missing heavy atom: .R.A

Added missing heavy atom: .R.A Added missing heavy atom: .R.A Creating new UNIT for residue: D sequence: 20 One sided connection. Residue: missing connect0 atom. Created a new atom named: H2' within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A

Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Joining DA - DT Created a new atom named: H5' within residue: .R

Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DC Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DC - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DG Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DG - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DT Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Joining DT - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DA Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DA - DC Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Joining DC - DC Created a new atom named: H5' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3T within residue: .R total atoms in file: 1146 Leap added 112 missing atoms according to residue templates: 27 Heavy 85 H / lone pairs The file contained 77 atoms not in residue templates > saveamberparm oligo.prmtop oligo.inpcrd saveAmberParm: Improper number of arguments! usage: saveAmberParm > saveamberparm mol1 oligo.prmtop oligo.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: -37.000000 is not zero. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R
.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. > quit Quit