log started: Thu May 5 21:26:05 2011 Log file: ./leap.log > # > # ----- leaprc for loading the ff03 (Duan et al.) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > # things should be there > { "IM" "Cl" "sp3" } > { "IP" "Na" "sp3" } > { "Li" "Li" "sp3" } > { "K" "K" "sp3" } > { "Rb" "Rb" "sp3" } > { "Cs" "Cs" "sp3" } > { "Zn" "Zn" "sp3" } > { "IB" "Na" "sp3" } > # "new" types > { "H0" "H" "sp3" } > > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /usr/local/amber11//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: LP) > frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /usr/local/amber11//dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions > > # > # Load water and ions > # > loadOff ions94.lib Loading library: /usr/local/amber11//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: /usr/local/amber11//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 > > # > # Load the existing 94 lib for nucleic acids and C- and N- terminal groups > # > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /usr/local/amber11//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_aminoct03.lib Loading library: /usr/local/amber11//dat/leap/lib/all_aminoct03.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS 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 > loadOff all_aminont03.lib Loading library: /usr/local/amber11//dat/leap/lib/all_aminont03.lib Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > loadOff all_amino03.lib Loading library: /usr/local/amber11//dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "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'" } > { "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" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > dna1=loadpdb "DNA.pdb" Loading PDB file: ./DNA.pdb Enter zPdbReadScan from call depth 0. -- residue 1: duplicate [ H2'] atoms (total 2) -- residue 1: duplicate [ H5'] atoms (total 2) -- residue 2: duplicate [ H2'] atoms (total 2) -- residue 2: duplicate [ H5'] atoms (total 2) -- residue 3: duplicate [ H2'] atoms (total 2) -- residue 3: duplicate [ H5'] atoms (total 2) -- residue 4: duplicate [ H2'] atoms (total 2) -- residue 4: duplicate [ H5'] atoms (total 2) -- residue 5: duplicate [ H2'] atoms (total 2) -- residue 5: duplicate [ H5'] atoms (total 2) -- residue 6: duplicate [ H2'] atoms (total 2) -- residue 6: duplicate [ H5'] atoms (total 2) -- residue 7: duplicate [ H2'] atoms (total 2) -- residue 7: duplicate [ H5'] atoms (total 2) -- residue 8: duplicate [ H2'] atoms (total 2) -- residue 8: duplicate [ H5'] atoms (total 2) -- residue 9: duplicate [ H2'] atoms (total 2) -- residue 9: duplicate [ H5'] atoms (total 2) -- residue 10: duplicate [ H2'] atoms (total 2) -- residue 10: duplicate [ H5'] atoms (total 2) -- residue 11: duplicate [ H2'] atoms (total 2) -- residue 11: duplicate [ H5'] atoms (total 2) -- residue 12: duplicate [ H2'] atoms (total 2) -- residue 12: duplicate [ H5'] atoms (total 2) -- residue 13: duplicate [ H2'] atoms (total 2) -- residue 13: duplicate [ H5'] atoms (total 2) -- residue 14: duplicate [ H2'] atoms (total 2) -- residue 14: duplicate [ H5'] atoms (total 2) -- residue 15: duplicate [ H2'] atoms (total 2) -- residue 15: duplicate [ H5'] atoms (total 2) -- residue 16: duplicate [ H2'] atoms (total 2) -- residue 16: duplicate [ H5'] atoms (total 2) -- residue 17: duplicate [ H2'] atoms (total 2) -- residue 17: duplicate [ H5'] atoms (total 2) -- residue 18: duplicate [ H2'] atoms (total 2) -- residue 18: duplicate [ H5'] atoms (total 2) -- residue 19: duplicate [ H2'] atoms (total 2) -- residue 19: duplicate [ H5'] atoms (total 2) -- residue 20: duplicate [ H2'] atoms (total 2) -- residue 20: duplicate [ H5'] atoms (total 2) -- residue 21: duplicate [ H2'] atoms (total 2) -- residue 21: duplicate [ H5'] atoms (total 2) -- residue 22: duplicate [ H2'] atoms (total 2) -- residue 22: duplicate [ H5'] atoms (total 2) -- residue 23: duplicate [ H2'] atoms (total 2) -- residue 23: duplicate [ H5'] atoms (total 2) -- residue 24: duplicate [ H2'] atoms (total 2) -- residue 24: duplicate [ H5'] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) 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 A, term: Nonterminal, seq. number: 3 to: RA. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue A, term: Nonterminal, seq. number: 5 to: RA. (Residue 6: T, Nonterminal, was not found in name map.) Unknown residue: T number: 6 type: Nonterminal (Residue 7: T, Nonterminal, was not found in name map.) Unknown residue: T number: 7 type: Nonterminal (Residue 8: T, Nonterminal, was not found in name map.) Unknown residue: T number: 8 type: Nonterminal Mapped residue G, term: Nonterminal, seq. number: 9 to: RG. Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue G, term: Terminal/last, seq. number: 11 to: RG3. Mapped residue C, term: Terminal/beginning, seq. number: 12 to: RC5. Mapped residue G, term: Nonterminal, seq. number: 13 to: RG. Mapped residue C, term: Nonterminal, seq. number: 14 to: RC. Mapped residue A, term: Nonterminal, seq. number: 15 to: RA. Mapped residue A, term: Nonterminal, seq. number: 16 to: RA. Mapped residue A, term: Nonterminal, seq. number: 17 to: RA. (Residue 18: T, Nonterminal, was not found in name map.) Unknown residue: T number: 18 type: Nonterminal (Residue 19: T, Nonterminal, was not found in name map.) Unknown residue: T number: 19 type: Nonterminal (Residue 20: T, Nonterminal, was not found in name map.) Unknown residue: T number: 20 type: Nonterminal Mapped residue C, term: Nonterminal, seq. number: 21 to: RC. Mapped residue G, term: Nonterminal, seq. number: 22 to: RG. Mapped residue C, term: Terminal/last, seq. number: 23 to: RC3. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Created a new atom named: HTE within residue: .R Added missing heavy atom: .R.A Joining RG5 - RC Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 7 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 8 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 9 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RG3 Created a new atom named: HCA within residue: .R Added missing heavy atom: .R.A Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Created a new atom named: HTE within residue: .R Added missing heavy atom: .R.A Joining RC5 - RG Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 19 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 20 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 21 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RC3 Created a new atom named: HCA within residue: .R Added missing heavy atom: .R.A total atoms in file: 768 Leap added 58 missing atoms according to residue templates: 18 Heavy 40 H / lone pairs The file contained 192 atoms not in residue templates > list ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TPF TRP TYR VAL WAT dna1 frcmod03 parm99 > help loadpdb variable = loadPdb filename STRING _filename_ Load a Protein Databank format file with the file name _filename_. The sequence numbers of the RESIDUEs will be determined from the order of residues within the PDB file ATOM records. For each residue in the PDB file, LEaP searches the variables currently defined for variable names that match the residue name. If a match is found, then the contents of the variable are copied into the UNIT created for the PDB structure. If no PDB `TER' card separates the current residue from the previous one, a bond is created between the connect1 ATOM of the previous residue and the connect0 atom of the new one. As atoms are read from the ATOM records, their coordinates are written into the correspondingly named ATOMs within the residue being built. If the entire residue is read and it is found that ATOM coordinates are missing, then external coordinates are built from the internal coordinates that were defined in the matching UNIT (residue) variable. This allows LEaP to build coordinates for hydrogens and lone pairs which are not specified in PDB files. > dna1 = loadpdb "DNA.pdb" Loading PDB file: ./DNA.pdb Enter zPdbReadScan from call depth 0. -- residue 1: duplicate [ H2'] atoms (total 2) -- residue 1: duplicate [ H5'] atoms (total 2) -- residue 2: duplicate [ H2'] atoms (total 2) -- residue 2: duplicate [ H5'] atoms (total 2) -- residue 3: duplicate [ H2'] atoms (total 2) -- residue 3: duplicate [ H5'] atoms (total 2) -- residue 4: duplicate [ H2'] atoms (total 2) -- residue 4: duplicate [ H5'] atoms (total 2) -- residue 5: duplicate [ H2'] atoms (total 2) -- residue 5: duplicate [ H5'] atoms (total 2) -- residue 6: duplicate [ H2'] atoms (total 2) -- residue 6: duplicate [ H5'] atoms (total 2) -- residue 7: duplicate [ H2'] atoms (total 2) -- residue 7: duplicate [ H5'] atoms (total 2) -- residue 8: duplicate [ H2'] atoms (total 2) -- residue 8: duplicate [ H5'] atoms (total 2) -- residue 9: duplicate [ H2'] atoms (total 2) -- residue 9: duplicate [ H5'] atoms (total 2) -- residue 10: duplicate [ H2'] atoms (total 2) -- residue 10: duplicate [ H5'] atoms (total 2) -- residue 11: duplicate [ H2'] atoms (total 2) -- residue 11: duplicate [ H5'] atoms (total 2) -- residue 12: duplicate [ H2'] atoms (total 2) -- residue 12: duplicate [ H5'] atoms (total 2) -- residue 13: duplicate [ H2'] atoms (total 2) -- residue 13: duplicate [ H5'] atoms (total 2) -- residue 14: duplicate [ H2'] atoms (total 2) -- residue 14: duplicate [ H5'] atoms (total 2) -- residue 15: duplicate [ H2'] atoms (total 2) -- residue 15: duplicate [ H5'] atoms (total 2) -- residue 16: duplicate [ H2'] atoms (total 2) -- residue 16: duplicate [ H5'] atoms (total 2) -- residue 17: duplicate [ H2'] atoms (total 2) -- residue 17: duplicate [ H5'] atoms (total 2) -- residue 18: duplicate [ H2'] atoms (total 2) -- residue 18: duplicate [ H5'] atoms (total 2) -- residue 19: duplicate [ H2'] atoms (total 2) -- residue 19: duplicate [ H5'] atoms (total 2) -- residue 20: duplicate [ H2'] atoms (total 2) -- residue 20: duplicate [ H5'] atoms (total 2) -- residue 21: duplicate [ H2'] atoms (total 2) -- residue 21: duplicate [ H5'] atoms (total 2) -- residue 22: duplicate [ H2'] atoms (total 2) -- residue 22: duplicate [ H5'] atoms (total 2) -- residue 23: duplicate [ H2'] atoms (total 2) -- residue 23: duplicate [ H5'] atoms (total 2) -- residue 24: duplicate [ H2'] atoms (total 2) -- residue 24: duplicate [ H5'] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) 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 A, term: Nonterminal, seq. number: 3 to: RA. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue A, term: Nonterminal, seq. number: 5 to: RA. (Residue 6: T, Nonterminal, was not found in name map.) Unknown residue: T number: 6 type: Nonterminal (Residue 7: T, Nonterminal, was not found in name map.) Unknown residue: T number: 7 type: Nonterminal (Residue 8: T, Nonterminal, was not found in name map.) Unknown residue: T number: 8 type: Nonterminal Mapped residue G, term: Nonterminal, seq. number: 9 to: RG. Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue G, term: Terminal/last, seq. number: 11 to: RG3. Mapped residue C, term: Terminal/beginning, seq. number: 12 to: RC5. Mapped residue G, term: Nonterminal, seq. number: 13 to: RG. Mapped residue C, term: Nonterminal, seq. number: 14 to: RC. Mapped residue A, term: Nonterminal, seq. number: 15 to: RA. Mapped residue A, term: Nonterminal, seq. number: 16 to: RA. Mapped residue A, term: Nonterminal, seq. number: 17 to: RA. (Residue 18: T, Nonterminal, was not found in name map.) Unknown residue: T number: 18 type: Nonterminal (Residue 19: T, Nonterminal, was not found in name map.) Unknown residue: T number: 19 type: Nonterminal (Residue 20: T, Nonterminal, was not found in name map.) Unknown residue: T number: 20 type: Nonterminal Mapped residue C, term: Nonterminal, seq. number: 21 to: RC. Mapped residue G, term: Nonterminal, seq. number: 22 to: RG. Mapped residue C, term: Terminal/last, seq. number: 23 to: RC3. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Created a new atom named: HTE within residue: .R Added missing heavy atom: .R.A Joining RG5 - RC Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 7 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 8 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 9 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RG3 Created a new atom named: HCA within residue: .R Added missing heavy atom: .R.A Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Created a new atom named: HTE within residue: .R Added missing heavy atom: .R.A Joining RC5 - RG Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 19 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 20 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 21 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RC3 Created a new atom named: HCA within residue: .R Added missing heavy atom: .R.A total atoms in file: 768 Leap added 58 missing atoms according to residue templates: 18 Heavy 40 H / lone pairs The file contained 192 atoms not in residue templates > dna1=loadpdb "DNA_1.pdb" Loading PDB file: ./DNA_1.pdb Enter zPdbReadScan from call depth 0. -- residue 1: duplicate [ H2'] atoms (total 2) -- residue 1: duplicate [ H5'] atoms (total 2) -- residue 2: duplicate [ H2'] atoms (total 2) -- residue 2: duplicate [ H5'] atoms (total 2) -- residue 3: duplicate [ H2'] atoms (total 2) -- residue 3: duplicate [ H5'] atoms (total 2) -- residue 4: duplicate [ H2'] atoms (total 2) -- residue 4: duplicate [ H5'] atoms (total 2) -- residue 5: duplicate [ H2'] atoms (total 2) -- residue 5: duplicate [ H5'] atoms (total 2) -- residue 6: duplicate [ H2'] atoms (total 2) -- residue 6: duplicate [ H5'] atoms (total 2) -- residue 7: duplicate [ H2'] atoms (total 2) -- residue 7: duplicate [ H5'] atoms (total 2) -- residue 8: duplicate [ H2'] atoms (total 2) -- residue 8: duplicate [ H5'] atoms (total 2) -- residue 9: duplicate [ H2'] atoms (total 2) -- residue 9: duplicate [ H5'] atoms (total 2) -- residue 10: duplicate [ H2'] atoms (total 2) -- residue 10: duplicate [ H5'] atoms (total 2) -- residue 11: duplicate [ H2'] atoms (total 2) -- residue 11: duplicate [ H5'] atoms (total 2) -- residue 12: duplicate [ H2'] atoms (total 2) -- residue 12: duplicate [ H5'] atoms (total 2) -- residue 13: duplicate [ H2'] atoms (total 2) -- residue 13: duplicate [ H5'] atoms (total 2) -- residue 14: duplicate [ H2'] atoms (total 2) -- residue 14: duplicate [ H5'] atoms (total 2) -- residue 15: duplicate [ H2'] atoms (total 2) -- residue 15: duplicate [ H5'] atoms (total 2) -- residue 16: duplicate [ H2'] atoms (total 2) -- residue 16: duplicate [ H5'] atoms (total 2) -- residue 17: duplicate [ H2'] atoms (total 2) -- residue 17: duplicate [ H5'] atoms (total 2) -- residue 18: duplicate [ H2'] atoms (total 2) -- residue 18: duplicate [ H5'] atoms (total 2) -- residue 19: duplicate [ H2'] atoms (total 2) -- residue 19: duplicate [ H5'] atoms (total 2) -- residue 20: duplicate [ H2'] atoms (total 2) -- residue 20: duplicate [ H5'] atoms (total 2) -- residue 21: duplicate [ H2'] atoms (total 2) -- residue 21: duplicate [ H5'] atoms (total 2) -- residue 22: duplicate [ H2'] atoms (total 2) -- residue 22: duplicate [ H5'] atoms (total 2) -- residue 23: duplicate [ H2'] atoms (total 2) -- residue 23: duplicate [ H5'] atoms (total 2) -- residue 24: duplicate [ H2'] atoms (total 2) -- residue 24: duplicate [ H5'] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) 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 A, term: Nonterminal, seq. number: 3 to: RA. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue A, term: Nonterminal, seq. number: 5 to: RA. (Residue 6: T, Nonterminal, was not found in name map.) Unknown residue: T number: 6 type: Nonterminal (Residue 7: T, Nonterminal, was not found in name map.) Unknown residue: T number: 7 type: Nonterminal (Residue 8: T, Nonterminal, was not found in name map.) Unknown residue: T number: 8 type: Nonterminal Mapped residue G, term: Nonterminal, seq. number: 9 to: RG. Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue G, term: Terminal/last, seq. number: 11 to: RG3. Mapped residue C, term: Terminal/beginning, seq. number: 12 to: RC5. Mapped residue G, term: Nonterminal, seq. number: 13 to: RG. Mapped residue C, term: Nonterminal, seq. number: 14 to: RC. Mapped residue A, term: Nonterminal, seq. number: 15 to: RA. Mapped residue A, term: Nonterminal, seq. number: 16 to: RA. Mapped residue A, term: Nonterminal, seq. number: 17 to: RA. (Residue 18: T, Nonterminal, was not found in name map.) Unknown residue: T number: 18 type: Nonterminal (Residue 19: T, Nonterminal, was not found in name map.) Unknown residue: T number: 19 type: Nonterminal (Residue 20: T, Nonterminal, was not found in name map.) Unknown residue: T number: 20 type: Nonterminal Mapped residue C, term: Nonterminal, seq. number: 21 to: RC. Mapped residue G, term: Nonterminal, seq. number: 22 to: RG. Mapped residue C, term: Terminal/last, seq. number: 23 to: RC3. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Created a new atom named: HTE within residue: .R Added missing heavy atom: .R.A Joining RG5 - RC Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 7 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 8 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 9 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RG3 Created a new atom named: HCA within residue: .R Added missing heavy atom: .R.A Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Created a new atom named: HTE within residue: .R Added missing heavy atom: .R.A Joining RC5 - RG Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 19 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 20 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 21 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RC3 Added missing heavy atom: .R.A total atoms in file: 767 Leap added 58 missing atoms according to residue templates: 18 Heavy 40 H / lone pairs The file contained 191 atoms not in residue templates > dna1=loadpdb "DNA_1pdb" Could not open file DNA_1pdb: not found > dna1=loadpdb "DNA_1.pdb" Loading PDB file: ./DNA_1.pdb Enter zPdbReadScan from call depth 0. -- residue 1: duplicate [ H2'] atoms (total 2) -- residue 1: duplicate [ H5'] atoms (total 2) -- residue 2: duplicate [ H2'] atoms (total 2) -- residue 2: duplicate [ H5'] atoms (total 2) -- residue 3: duplicate [ H2'] atoms (total 2) -- residue 3: duplicate [ H5'] atoms (total 2) -- residue 4: duplicate [ H2'] atoms (total 2) -- residue 4: duplicate [ H5'] atoms (total 2) -- residue 5: duplicate [ H2'] atoms (total 2) -- residue 5: duplicate [ H5'] atoms (total 2) -- residue 6: duplicate [ H2'] atoms (total 2) -- residue 6: duplicate [ H5'] atoms (total 2) -- residue 7: duplicate [ H2'] atoms (total 2) -- residue 7: duplicate [ H5'] atoms (total 2) -- residue 8: duplicate [ H2'] atoms (total 2) -- residue 8: duplicate [ H5'] atoms (total 2) -- residue 9: duplicate [ H2'] atoms (total 2) -- residue 9: duplicate [ H5'] atoms (total 2) -- residue 10: duplicate [ H2'] atoms (total 2) -- residue 10: duplicate [ H5'] atoms (total 2) -- residue 11: duplicate [ H2'] atoms (total 2) -- residue 11: duplicate [ H5'] atoms (total 2) -- residue 12: duplicate [ H2'] atoms (total 2) -- residue 12: duplicate [ H5'] atoms (total 2) -- residue 13: duplicate [ H2'] atoms (total 2) -- residue 13: duplicate [ H5'] atoms (total 2) -- residue 14: duplicate [ H2'] atoms (total 2) -- residue 14: duplicate [ H5'] atoms (total 2) -- residue 15: duplicate [ H2'] atoms (total 2) -- residue 15: duplicate [ H5'] atoms (total 2) -- residue 16: duplicate [ H2'] atoms (total 2) -- residue 16: duplicate [ H5'] atoms (total 2) -- residue 17: duplicate [ H2'] atoms (total 2) -- residue 17: duplicate [ H5'] atoms (total 2) -- residue 18: duplicate [ H2'] atoms (total 2) -- residue 18: duplicate [ H5'] atoms (total 2) -- residue 19: duplicate [ H2'] atoms (total 2) -- residue 19: duplicate [ H5'] atoms (total 2) -- residue 20: duplicate [ H2'] atoms (total 2) -- residue 20: duplicate [ H5'] atoms (total 2) -- residue 21: duplicate [ H2'] atoms (total 2) -- residue 21: duplicate [ H5'] atoms (total 2) -- residue 22: duplicate [ H2'] atoms (total 2) -- residue 22: duplicate [ H5'] atoms (total 2) -- residue 23: duplicate [ H2'] atoms (total 2) -- residue 23: duplicate [ H5'] atoms (total 2) -- residue 24: duplicate [ H2'] atoms (total 2) -- residue 24: duplicate [ H5'] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) 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 A, term: Nonterminal, seq. number: 3 to: RA. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue A, term: Nonterminal, seq. number: 5 to: RA. (Residue 6: T, Nonterminal, was not found in name map.) Unknown residue: T number: 6 type: Nonterminal (Residue 7: T, Nonterminal, was not found in name map.) Unknown residue: T number: 7 type: Nonterminal (Residue 8: T, Nonterminal, was not found in name map.) Unknown residue: T number: 8 type: Nonterminal Mapped residue G, term: Nonterminal, seq. number: 9 to: RG. Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue G, term: Terminal/last, seq. number: 11 to: RG3. Mapped residue C, term: Terminal/beginning, seq. number: 12 to: RC5. Mapped residue G, term: Nonterminal, seq. number: 13 to: RG. Mapped residue C, term: Nonterminal, seq. number: 14 to: RC. Mapped residue A, term: Nonterminal, seq. number: 15 to: RA. Mapped residue A, term: Nonterminal, seq. number: 16 to: RA. Mapped residue A, term: Nonterminal, seq. number: 17 to: RA. (Residue 18: T, Nonterminal, was not found in name map.) Unknown residue: T number: 18 type: Nonterminal (Residue 19: T, Nonterminal, was not found in name map.) Unknown residue: T number: 19 type: Nonterminal (Residue 20: T, Nonterminal, was not found in name map.) Unknown residue: T number: 20 type: Nonterminal Mapped residue C, term: Nonterminal, seq. number: 21 to: RC. Mapped residue G, term: Nonterminal, seq. number: 22 to: RG. Mapped residue C, term: Terminal/last, seq. number: 23 to: RC3. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Added missing heavy atom: .R.A Joining RG5 - RC Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 7 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 8 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 9 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RG3 Added missing heavy atom: .R.A Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Added missing heavy atom: .R.A Joining RC5 - RG Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 19 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 20 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 21 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RC3 Added missing heavy atom: .R.A total atoms in file: 764 Leap added 58 missing atoms according to residue templates: 18 Heavy 40 H / lone pairs The file contained 188 atoms not in residue templates > help list for thymine help: Improper number of arguments! usage: help > help list list List all of the variables currently defined. > list ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX Cl- Cs+ DA DA3 DA5 DAN DC DC3 DC4 DC5 DCN DG DG3 DG5 DGN DT DT3 DT5 DTN GLH GLN GLU GLY HID HIE HIP HIS HOH IB ILE K+ LEU LYN LYS Li+ MEOHBOX MET MG2 NALA NARG NASN NASP NCYS NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5 RAN RC RC3 RC5 RCN RG RG3 RG5 RGN RU RU3 RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOXTP3 TP4 TP5 TPF TRP TYR VAL WAT dna1 frcmod03 parm99 log started: Fri May 6 15:17:06 2011 Log file: ./leap.log > # > # ----- leaprc for loading the ff03 (Duan et al.) force field > # > # load atom type hybridizations > # > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H1" "H" "sp3" } > { "H2" "H" "sp3" } > { "H3" "H" "sp3" } > { "H4" "H" "sp3" } > { "H5" "H" "sp3" } > { "HW" "H" "sp3" } > { "HC" "H" "sp3" } > { "HA" "H" "sp3" } > { "HP" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CH" "C" "sp3" } > { "C2" "C" "sp3" } > { "C3" "C" "sp3" } > { "C" "C" "sp2" } > { "C*" "C" "sp2" } > { "CA" "C" "sp2" } > { "CB" "C" "sp2" } > { "CC" "C" "sp2" } > { "CN" "C" "sp2" } > { "CM" "C" "sp2" } > { "CK" "C" "sp2" } > { "CQ" "C" "sp2" } > { "CD" "C" "sp2" } > { "CE" "C" "sp2" } > { "CF" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp2" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "C" "sp2" } > { "MG" "Mg" "sp3" } > { "N" "N" "sp2" } > { "NA" "N" "sp2" } > { "N2" "N" "sp2" } > { "N*" "N" "sp2" } > { "NP" "N" "sp2" } > { "NQ" "N" "sp2" } > { "NB" "N" "sp2" } > { "NC" "N" "sp2" } > { "NT" "N" "sp3" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "F" "F" "sp3" } > { "CL" "Cl" "sp3" } > { "BR" "Br" "sp3" } > { "I" "I" "sp3" } > { "FE" "Fe" "sp3" } > # things should be there > { "IM" "Cl" "sp3" } > { "IP" "Na" "sp3" } > { "Li" "Li" "sp3" } > { "K" "K" "sp3" } > { "Rb" "Rb" "sp3" } > { "Cs" "Cs" "sp3" } > { "Zn" "Zn" "sp3" } > { "IB" "Na" "sp3" } > # "new" types > { "H0" "H" "sp3" } > > } > # > # Load the main parameter set. > # > parm99 = loadamberparams parm99.dat Loading parameters: /usr/local/amber11//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: LP) > frcmod03 = loadamberparams frcmod.ff03 Loading parameters: /usr/local/amber11//dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions > > # > # Load water and ions > # > loadOff ions94.lib Loading library: /usr/local/amber11//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: /usr/local/amber11//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 > > # > # Load the existing 94 lib for nucleic acids and C- and N- terminal groups > # > # > # Load DNA/RNA libraries > # > loadOff all_nucleic94.lib Loading library: /usr/local/amber11//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_aminoct03.lib Loading library: /usr/local/amber11//dat/leap/lib/all_aminoct03.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS 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 > loadOff all_aminont03.lib Loading library: /usr/local/amber11//dat/leap/lib/all_aminont03.lib Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL > loadOff all_amino03.lib Loading library: /usr/local/amber11//dat/leap/lib/all_amino03.lib Loading: ACE Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: NHE Loading: NME Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL > > > # > # Define the PDB name map for the amino acids and DNA. > # > addPdbResMap { > { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } > { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } > { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } > { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } > { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } > { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } > { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } > { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } > { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } > { 0 "HID" "NHID" } { 1 "HID" "CHID" } > { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } > { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } > { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } > { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } > { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } > { 0 "MET" "NMET" } { 1 "MET" "CMET" } > { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } > { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } > { 0 "SER" "NSER" } { 1 "SER" "CSER" } > { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } > { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } > { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } > { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } > { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } > { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } > { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } > { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } > { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } > { 0 "G" "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'" } > { "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" } > } > > > # > # assumed that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE > close ERROR: syntax error > exit ERROR: syntax error > Close ERROR: syntax error log started: Fri May 6 15:22:28 2011 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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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 > dna1=loadpdb "DNA_1.pdb" Loading PDB file: ./DNA_1.pdb Enter zPdbReadScan from call depth 0. -- residue 1: duplicate [ H2'] atoms (total 2) -- residue 1: duplicate [ H5'] atoms (total 2) -- residue 2: duplicate [ H2'] atoms (total 2) -- residue 2: duplicate [ H5'] atoms (total 2) -- residue 3: duplicate [ H2'] atoms (total 2) -- residue 3: duplicate [ H5'] atoms (total 2) -- residue 4: duplicate [ H2'] atoms (total 2) -- residue 4: duplicate [ H5'] atoms (total 2) -- residue 5: duplicate [ H2'] atoms (total 2) -- residue 5: duplicate [ H5'] atoms (total 2) -- residue 6: duplicate [ H2'] atoms (total 2) -- residue 6: duplicate [ H5'] atoms (total 2) -- residue 7: duplicate [ H2'] atoms (total 2) -- residue 7: duplicate [ H5'] atoms (total 2) -- residue 8: duplicate [ H2'] atoms (total 2) -- residue 8: duplicate [ H5'] atoms (total 2) -- residue 9: duplicate [ H2'] atoms (total 2) -- residue 9: duplicate [ H5'] atoms (total 2) -- residue 10: duplicate [ H2'] atoms (total 2) -- residue 10: duplicate [ H5'] atoms (total 2) -- residue 11: duplicate [ H2'] atoms (total 2) -- residue 11: duplicate [ H5'] atoms (total 2) -- residue 12: duplicate [ H2'] atoms (total 2) -- residue 12: duplicate [ H5'] atoms (total 2) -- residue 13: duplicate [ H2'] atoms (total 2) -- residue 13: duplicate [ H5'] atoms (total 2) -- residue 14: duplicate [ H2'] atoms (total 2) -- residue 14: duplicate [ H5'] atoms (total 2) -- residue 15: duplicate [ H2'] atoms (total 2) -- residue 15: duplicate [ H5'] atoms (total 2) -- residue 16: duplicate [ H2'] atoms (total 2) -- residue 16: duplicate [ H5'] atoms (total 2) -- residue 17: duplicate [ H2'] atoms (total 2) -- residue 17: duplicate [ H5'] atoms (total 2) -- residue 18: duplicate [ H2'] atoms (total 2) -- residue 18: duplicate [ H5'] atoms (total 2) -- residue 19: duplicate [ H2'] atoms (total 2) -- residue 19: duplicate [ H5'] atoms (total 2) -- residue 20: duplicate [ H2'] atoms (total 2) -- residue 20: duplicate [ H5'] atoms (total 2) -- residue 21: duplicate [ H2'] atoms (total 2) -- residue 21: duplicate [ H5'] atoms (total 2) -- residue 22: duplicate [ H2'] atoms (total 2) -- residue 22: duplicate [ H5'] atoms (total 2) -- residue 23: duplicate [ H2'] atoms (total 2) -- residue 23: duplicate [ H5'] atoms (total 2) -- residue 24: duplicate [ H2'] atoms (total 2) -- residue 24: duplicate [ H5'] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) 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 A, term: Nonterminal, seq. number: 3 to: RA. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue A, term: Nonterminal, seq. number: 5 to: RA. (Residue 6: T, Nonterminal, was not found in name map.) Unknown residue: T number: 6 type: Nonterminal (Residue 7: T, Nonterminal, was not found in name map.) Unknown residue: T number: 7 type: Nonterminal (Residue 8: T, Nonterminal, was not found in name map.) Unknown residue: T number: 8 type: Nonterminal Mapped residue G, term: Nonterminal, seq. number: 9 to: RG. Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue G, term: Terminal/last, seq. number: 11 to: RG3. Mapped residue C, term: Terminal/beginning, seq. number: 12 to: RC5. Mapped residue G, term: Nonterminal, seq. number: 13 to: RG. Mapped residue C, term: Nonterminal, seq. number: 14 to: RC. Mapped residue A, term: Nonterminal, seq. number: 15 to: RA. Mapped residue A, term: Nonterminal, seq. number: 16 to: RA. Mapped residue A, term: Nonterminal, seq. number: 17 to: RA. (Residue 18: T, Nonterminal, was not found in name map.) Unknown residue: T number: 18 type: Nonterminal (Residue 19: T, Nonterminal, was not found in name map.) Unknown residue: T number: 19 type: Nonterminal (Residue 20: T, Nonterminal, was not found in name map.) Unknown residue: T number: 20 type: Nonterminal Mapped residue C, term: Nonterminal, seq. number: 21 to: RC. Mapped residue G, term: Nonterminal, seq. number: 22 to: RG. Mapped residue C, term: Terminal/last, seq. number: 23 to: RC3. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Added missing heavy atom: .R.A Joining RG5 - RC Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 7 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 8 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 9 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RG3 Added missing heavy atom: .R.A Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Added missing heavy atom: .R.A Joining RC5 - RG Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 19 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 20 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 21 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RC3 Added missing heavy atom: .R.A total atoms in file: 763 Leap added 58 missing atoms according to residue templates: 18 Heavy 40 H / lone pairs The file contained 187 atoms not in residue templates > dna1=loadpdb "DNA_1.pdb" Loading PDB file: ./DNA_1.pdb Enter zPdbReadScan from call depth 0. -- residue 1: duplicate [ H2'] atoms (total 2) -- residue 1: duplicate [ H5'] atoms (total 2) -- residue 2: duplicate [ H2'] atoms (total 2) -- residue 2: duplicate [ H5'] atoms (total 2) -- residue 3: duplicate [ H2'] atoms (total 2) -- residue 3: duplicate [ H5'] atoms (total 2) -- residue 4: duplicate [ H2'] atoms (total 2) -- residue 4: duplicate [ H5'] atoms (total 2) -- residue 5: duplicate [ H2'] atoms (total 2) -- residue 5: duplicate [ H5'] atoms (total 2) -- residue 6: duplicate [ H2'] atoms (total 2) -- residue 6: duplicate [ H5'] atoms (total 2) -- residue 7: duplicate [ H2'] atoms (total 2) -- residue 7: duplicate [ H5'] atoms (total 2) -- residue 8: duplicate [ H2'] atoms (total 2) -- residue 8: duplicate [ H5'] atoms (total 2) -- residue 9: duplicate [ H2'] atoms (total 2) -- residue 9: duplicate [ H5'] atoms (total 2) -- residue 10: duplicate [ H2'] atoms (total 2) -- residue 10: duplicate [ H5'] atoms (total 2) -- residue 11: duplicate [ H2'] atoms (total 2) -- residue 11: duplicate [ H5'] atoms (total 2) -- residue 12: duplicate [ H2'] atoms (total 2) -- residue 12: duplicate [ H5'] atoms (total 2) -- residue 13: duplicate [ H2'] atoms (total 2) -- residue 13: duplicate [ H5'] atoms (total 2) -- residue 14: duplicate [ H2'] atoms (total 2) -- residue 14: duplicate [ H5'] atoms (total 2) -- residue 15: duplicate [ H2'] atoms (total 2) -- residue 15: duplicate [ H5'] atoms (total 2) -- residue 16: duplicate [ H2'] atoms (total 2) -- residue 16: duplicate [ H5'] atoms (total 2) -- residue 17: duplicate [ H2'] atoms (total 2) -- residue 17: duplicate [ H5'] atoms (total 2) -- residue 18: duplicate [ H2'] atoms (total 2) -- residue 18: duplicate [ H5'] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) 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 A, term: Nonterminal, seq. number: 3 to: RA. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue A, term: Nonterminal, seq. number: 5 to: RA. Mapped residue G, term: Nonterminal, seq. number: 6 to: RG. Mapped residue C, term: Nonterminal, seq. number: 7 to: RC. Mapped residue G, term: Terminal/last, seq. number: 8 to: RG3. Mapped residue C, term: Terminal/beginning, seq. number: 9 to: RC5. Mapped residue G, term: Nonterminal, seq. number: 10 to: RG. Mapped residue C, term: Nonterminal, seq. number: 11 to: RC. Mapped residue A, term: Nonterminal, seq. number: 12 to: RA. Mapped residue A, term: Nonterminal, seq. number: 13 to: RA. Mapped residue A, term: Nonterminal, seq. number: 14 to: RA. Mapped residue C, term: Nonterminal, seq. number: 15 to: RC. Mapped residue G, term: Nonterminal, seq. number: 16 to: RG. Mapped residue C, term: Terminal/last, seq. number: 17 to: RC3. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Added missing heavy atom: .R.A Joining RG5 - RC Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RG Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RG3 Added missing heavy atom: .R.A Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Added missing heavy atom: .R.A Joining RC5 - RG Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RC Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RC3 Added missing heavy atom: .R.A total atoms in file: 572 Leap added 58 missing atoms according to residue templates: 18 Heavy 40 H / lone pairs The file contained 8 atoms not in residue templates log started: Sat May 7 01:28:03 2011 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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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: /usr/local/amber11//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 > dna1=loadpdb "DNA.pdb" Loading PDB file: ./DNA.pdb Enter zPdbReadScan from call depth 0. -- residue 1: duplicate [ H2'] atoms (total 2) -- residue 1: duplicate [ H5'] atoms (total 2) -- residue 2: duplicate [ H2'] atoms (total 2) -- residue 2: duplicate [ H5'] atoms (total 2) -- residue 3: duplicate [ H2'] atoms (total 2) -- residue 3: duplicate [ H5'] atoms (total 2) -- residue 4: duplicate [ H2'] atoms (total 2) -- residue 4: duplicate [ H5'] atoms (total 2) -- residue 5: duplicate [ H2'] atoms (total 2) -- residue 5: duplicate [ H5'] atoms (total 2) -- residue 6: duplicate [ H2'] atoms (total 2) -- residue 6: duplicate [ H5'] atoms (total 2) -- residue 7: duplicate [ H2'] atoms (total 2) -- residue 7: duplicate [ H5'] atoms (total 2) -- residue 8: duplicate [ H2'] atoms (total 2) -- residue 8: duplicate [ H5'] atoms (total 2) -- residue 9: duplicate [ H2'] atoms (total 2) -- residue 9: duplicate [ H5'] atoms (total 2) -- residue 10: duplicate [ H2'] atoms (total 2) -- residue 10: duplicate [ H5'] atoms (total 2) -- residue 11: duplicate [ H2'] atoms (total 2) -- residue 11: duplicate [ H5'] atoms (total 2) -- residue 12: duplicate [ H2'] atoms (total 2) -- residue 12: duplicate [ H5'] atoms (total 2) -- residue 13: duplicate [ H2'] atoms (total 2) -- residue 13: duplicate [ H5'] atoms (total 2) -- residue 14: duplicate [ H2'] atoms (total 2) -- residue 14: duplicate [ H5'] atoms (total 2) -- residue 15: duplicate [ H2'] atoms (total 2) -- residue 15: duplicate [ H5'] atoms (total 2) -- residue 16: duplicate [ H2'] atoms (total 2) -- residue 16: duplicate [ H5'] atoms (total 2) -- residue 17: duplicate [ H2'] atoms (total 2) -- residue 17: duplicate [ H5'] atoms (total 2) -- residue 18: duplicate [ H2'] atoms (total 2) -- residue 18: duplicate [ H5'] atoms (total 2) -- residue 19: duplicate [ H2'] atoms (total 2) -- residue 19: duplicate [ H5'] atoms (total 2) -- residue 20: duplicate [ H2'] atoms (total 2) -- residue 20: duplicate [ H5'] atoms (total 2) -- residue 21: duplicate [ H2'] atoms (total 2) -- residue 21: duplicate [ H5'] atoms (total 2) -- residue 22: duplicate [ H2'] atoms (total 2) -- residue 22: duplicate [ H5'] atoms (total 2) -- residue 23: duplicate [ H2'] atoms (total 2) -- residue 23: duplicate [ H5'] atoms (total 2) -- residue 24: duplicate [ H2'] atoms (total 2) -- residue 24: duplicate [ H5'] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) 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 A, term: Nonterminal, seq. number: 3 to: RA. Mapped residue A, term: Nonterminal, seq. number: 4 to: RA. Mapped residue A, term: Nonterminal, seq. number: 5 to: RA. (Residue 6: T, Nonterminal, was not found in name map.) Unknown residue: T number: 6 type: Nonterminal (Residue 7: T, Nonterminal, was not found in name map.) Unknown residue: T number: 7 type: Nonterminal (Residue 8: T, Nonterminal, was not found in name map.) Unknown residue: T number: 8 type: Nonterminal Mapped residue G, term: Nonterminal, seq. number: 9 to: RG. Mapped residue C, term: Nonterminal, seq. number: 10 to: RC. Mapped residue G, term: Terminal/last, seq. number: 11 to: RG3. Mapped residue C, term: Terminal/beginning, seq. number: 12 to: RC5. Mapped residue G, term: Nonterminal, seq. number: 13 to: RG. Mapped residue C, term: Nonterminal, seq. number: 14 to: RC. Mapped residue A, term: Nonterminal, seq. number: 15 to: RA. Mapped residue A, term: Nonterminal, seq. number: 16 to: RA. Mapped residue A, term: Nonterminal, seq. number: 17 to: RA. (Residue 18: T, Nonterminal, was not found in name map.) Unknown residue: T number: 18 type: Nonterminal (Residue 19: T, Nonterminal, was not found in name map.) Unknown residue: T number: 19 type: Nonterminal (Residue 20: T, Nonterminal, was not found in name map.) Unknown residue: T number: 20 type: Nonterminal Mapped residue C, term: Nonterminal, seq. number: 21 to: RC. Mapped residue G, term: Nonterminal, seq. number: 22 to: RG. Mapped residue C, term: Terminal/last, seq. number: 23 to: RC3. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Created a new atom named: HTE within residue: .R Added missing heavy atom: .R.A Joining RG5 - RC Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 7 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 8 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 9 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RG3 Created a new atom named: HCA within residue: .R Added missing heavy atom: .R.A Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: OXT within residue: .R Created a new atom named: HTE within residue: .R Added missing heavy atom: .R.A Joining RC5 - RG Added missing heavy atom: .R.A Joining RG - RC Added missing heavy atom: .R.A Joining RC - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Joining RA - RA Added missing heavy atom: .R.A Creating new UNIT for residue: T sequence: 19 One sided connection. Residue: missing connect0 atom. Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 20 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R Creating new UNIT for residue: T sequence: 21 Starting new chain with Created a new atom named: P within residue: .R Created a new atom named: O1P within residue: .R Created a new atom named: O2P within residue: .R Created a new atom named: O5' within residue: .R Created a new atom named: C5' within residue: .R Created a new atom named: C4' within residue: .R Created a new atom named: O4' within residue: .R Created a new atom named: C3' within residue: .R Created a new atom named: O3' within residue: .R Created a new atom named: C2' within residue: .R Created a new atom named: C1' within residue: .R Created a new atom named: N1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: O2 within residue: .R Created a new atom named: N3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: O4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C5M within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: H5' within residue: .R Created a new atom named: H4' within residue: .R Created a new atom named: H1' within residue: .R Created a new atom named: H2' within residue: .R Created a new atom named: H3' within residue: .R Created a new atom named: H6 within residue: .R Created a new atom named: H3 within residue: .R Created a new atom named: H51 within residue: .R Created a new atom named: H52 within residue: .R Created a new atom named: H53 within residue: .R One sided connection. Residue: missing connect1 atom. Added missing heavy atom: .R.A Joining RC - RG Added missing heavy atom: .R.A Joining RG - RC3 Created a new atom named: HCA within residue: .R Added missing heavy atom: .R.A total atoms in file: 768 Leap added 58 missing atoms according to residue templates: 18 Heavy 40 H / lone pairs The file contained 192 atoms not in residue templates