log started: Thu Dec 13 15:54:26 2001 Log file: ./leap.log >> # >> # ----- leaprc for loading the Cornell et al. 1994 force field. >> # assumes that any unspecified nucleic acids are DNA >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm94 = loadamberparams parm94.dat Loading parameters: /thr/gamow/amber7/dat/parm94.dat (UNKNOWN ATOM TYPE: HV) (UNKNOWN ATOM TYPE: OV) (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: IB) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /thr/gamow/amber7/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_amino94.lib Loading library: /thr/gamow/amber7/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: /thr/gamow/amber7/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: /thr/gamow/amber7/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> loadOff ions94.lib Loading library: /thr/gamow/amber7/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: Na+ Loading: Rb+ >> # >> # Load water library containing TIP3 UNIT (WAT) and WATBOX216 periodic >> # box of 216 TIP3s. >> # >> loadOff water.lib Loading library: /thr/gamow/amber7/dat/leap/lib/water.lib Loading: TIP3 Loading: WAT Loading: WATBOX216 >> HOH = WAT >> TIP3 = WAT >> IP3 = WAT >> >> >> # >> # 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" "DG" } { 1 "GUA" "DG" } { "GUA" "DG" } >> { 0 "ADE" "DA" } { 1 "ADE" "DA" } { "ADE" "DA" } >> { 0 "CYT" "DC" } { 1 "CYT" "DC" } { "CYT" "DC" } >> { 0 "THY" "DT" } { 1 "THY" "DT" } { "THY" "DT" } >> { 0 " G" "DG" } { 1 " G" "DG" } { " G" "DG" } >> { 0 " A" "DA" } { 1 " A" "DA" } { " A" "DA" } >> { 0 " C" "DC" } { 1 " C" "DC" } { " C" "DC" } >> { 0 " T" "DT" } { 1 " T" "DT" } { " T" "DT" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> # >> # assumed that most often users will want to use HID >> # >> NHIS = NHID >> HIS = HID >> CHIS = CHID >> >> # Aliases >> alias a alias >> a q quit >> a exit quit >> a ? help >> a e edit >> a s source >> a seq sequence >> # Aliases abbreviated w/ verbs 1st >> a l loadOff >> a lp loadPdb >> a so saveOff >> a sop saveOffParm >> a sap saveAmberParm >> a sp savePdb >> a ap loadAmberParams >> a lap loadAmberPrep >> a ai addIons > > help set set default variable value STRING _variable_ STRING _value_ OR set container parameter object UNIT/RESIDUE/ATOM/STRING _container_ STRING _parameter_ object _object/value_ This command sets the values of some global parameters (when the first argument is "default") or sets various parameters associated with _container_. The possible variables for "set default" are: PdbWriteCharges "on" add charges to each ATOM record "off" don't do this (default) OldPrmtopFormat "on" use prmtop format from Amber6 and earlier "off" use the new prmtop format (default) GBParm "bondi" use Bondi radii for generalized Born (default) "mbondi" use modified Bondi radii (see Users' Manual for details) Dielectric "distance" use distance-dependent dielectric (default) "constant" use constant dielectric The more useful parameters for each type of _container_ are: container attributes values UNIT name STRING head, tail ATOM [e.g. unit.1.1] restype "protein" "nucleic" "saccharide" "solvent" "undefined" [sets all residues in UNIT] cap LIST [center, radius: {X Y Z R}] or "null" RESIDUE name STRING [e.g. restype [see UNIT] unit.1] connect0, connect1 ATOM [e.g. unit.1.1] imagingAtom ATOM [e.g. unit.1.1] ATOM name, pertName STRING [<= 4 chars] [e.g. type, pertType STRING [<= 2 chars] unit.1.1] element STRING pert "true" [or pert flag unset] charge, pertCharge DOUBLE position LIST [{X Y Z}] > set default GBParm mbondi can't parse gbparm usage: set or: set default > set default gbparm mbondi can't parse gbparm usage: set or: set default > set default pbradii mbondi Using modified Bondi radii > x = loadpdb circ.pdb Loading PDB file: ./circ.pdb Matching PDB residue names to LEaP variables. Mapped residue CYT, term: Terminal/beginning, seq. number: 0 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 1 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 2 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 3 to: DT. Mapped residue ADE, term: Nonterminal, seq. number: 4 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 5 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 6 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 7 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 8 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 9 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 10 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 11 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 12 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 13 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 14 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 15 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 16 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 17 to: DA. Mapped residue THY, term: Nonterminal, seq. number: 18 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 19 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 20 to: DA. Mapped residue ADE, term: Nonterminal, seq. number: 21 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 22 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 23 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 24 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 25 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 26 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 27 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 28 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 29 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 30 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 31 to: DT. Mapped residue ADE, term: Nonterminal, seq. number: 32 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 33 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 34 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 35 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 36 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 37 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 38 to: DT. Mapped residue ADE, term: Nonterminal, seq. number: 39 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 40 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 41 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 42 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 43 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 44 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 45 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 46 to: DA. Mapped residue ADE, term: Nonterminal, seq. number: 47 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 48 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 49 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 50 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 51 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 52 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 53 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 54 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 55 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 56 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 57 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 58 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 59 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 60 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 61 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 62 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 63 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 64 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 65 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 66 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 67 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 68 to: DT. Mapped residue ADE, term: Nonterminal, seq. number: 69 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 70 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 71 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 72 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 73 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 74 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 75 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 76 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 77 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 78 to: DA. Mapped residue THY, term: Nonterminal, seq. number: 79 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 80 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 81 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 82 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 83 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 84 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 85 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 86 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 87 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 88 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 89 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 90 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 91 to: DA. Mapped residue ADE, term: Nonterminal, seq. number: 92 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 93 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 94 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 95 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 96 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 97 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 98 to: DG. Mapped residue GUA, term: Terminal/last, seq. number: 99 to: DG. Mapped residue CYT, term: Terminal/beginning, seq. number: 100 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 101 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 102 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 103 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 104 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 105 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 106 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 107 to: DT. Mapped residue THY, term: Nonterminal, seq. number: 108 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 109 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 110 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 111 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 112 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 113 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 114 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 115 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 116 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 117 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 118 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 119 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 120 to: DA. Mapped residue THY, term: Nonterminal, seq. number: 121 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 122 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 123 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 124 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 125 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 126 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 127 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 128 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 129 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 130 to: DT. Mapped residue ADE, term: Nonterminal, seq. number: 131 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 132 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 133 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 134 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 135 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 136 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 137 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 138 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 139 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 140 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 141 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 142 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 143 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 144 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 145 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 146 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 147 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 148 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 149 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 150 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 151 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 152 to: DT. Mapped residue THY, term: Nonterminal, seq. number: 153 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 154 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 155 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 156 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 157 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 158 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 159 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 160 to: DT. Mapped residue ADE, term: Nonterminal, seq. number: 161 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 162 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 163 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 164 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 165 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 166 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 167 to: DT. Mapped residue ADE, term: Nonterminal, seq. number: 168 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 169 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 170 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 171 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 172 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 173 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 174 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 175 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 176 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 177 to: DC. Mapped residue THY, term: Nonterminal, seq. number: 178 to: DT. Mapped residue THY, term: Nonterminal, seq. number: 179 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 180 to: DC. Mapped residue ADE, term: Nonterminal, seq. number: 181 to: DA. Mapped residue THY, term: Nonterminal, seq. number: 182 to: DT. Mapped residue GUA, term: Nonterminal, seq. number: 183 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 184 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 185 to: DG. Mapped residue ADE, term: Nonterminal, seq. number: 186 to: DA. Mapped residue CYT, term: Nonterminal, seq. number: 187 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 188 to: DG. Mapped residue CYT, term: Nonterminal, seq. number: 189 to: DC. Mapped residue CYT, term: Nonterminal, seq. number: 190 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 191 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 192 to: DT. Mapped residue CYT, term: Nonterminal, seq. number: 193 to: DC. Mapped residue GUA, term: Nonterminal, seq. number: 194 to: DG. Mapped residue THY, term: Nonterminal, seq. number: 195 to: DT. Mapped residue ADE, term: Nonterminal, seq. number: 196 to: DA. Mapped residue GUA, term: Nonterminal, seq. number: 197 to: DG. Mapped residue GUA, term: Nonterminal, seq. number: 198 to: DG. Mapped residue GUA, term: Terminal/last, seq. number: 199 to: DG. Joining DC - DC Joining DC - DC Joining DC - DT Joining DT - DA Joining DA - DC Joining DC - DG Joining DG - DA Joining DA - DC Joining DC - DG Joining DG - DG Joining DG - DC Joining DC - DG Joining DG - DT Joining DT - DC Joining DC - DC Joining DC - DC Joining DC - DA Joining DA - DT Joining DT - DG Joining DG - DA Joining DA - DA Joining DA - DG Joining DG - DG Joining DG - DC Joining DC - DG Joining DG - DG Joining DG - DG Joining DG - DG Joining DG - DG Joining DG - DC Joining DC - DT Joining DT - DA Joining DA - DG Joining DG - DA Joining DA - DC Joining DC - DA Joining DA - DC Joining DC - DT Joining DT - DA Joining DA - DG Joining DG - DG Joining DG - DA Joining DA - DG Joining DG - DC Joining DC - DG Joining DG - DA Joining DA - DA Joining DA - DG Joining DG - DA Joining DA - DC Joining DC - DA Joining DA - DC Joining DC - DA Joining DA - DG Joining DG - DA Joining DA - DG Joining DG - DC Joining DC - DA Joining DA - DG Joining DG - DT Joining DT - DG Joining DG - DC Joining DC - DG Joining DG - DG Joining DG - DG Joining DG - DA Joining DA - DG Joining DG - DT Joining DT - DA Joining DA - DG Joining DG - DA Joining DA - DG Joining DG - DG Joining DG - DA Joining DA - DC Joining DC - DA Joining DA - DG Joining DG - DA Joining DA - DT Joining DT - DG Joining DG - DC Joining DC - DC Joining DC - DA Joining DA - DG Joining DG - DC Joining DC - DG Joining DG - DG Joining DG - DG Joining DG - DC Joining DC - DG Joining DG - DA Joining DA - DA Joining DA - DC Joining DC - DA Joining DA - DC Joining DC - DA Joining DA - DG Joining DG - DG Joining DG - DG Joining DC - DC Joining DC - DC Joining DC - DT Joining DT - DG Joining DG - DT Joining DT - DG Joining DG - DT Joining DT - DT Joining DT - DC Joining DC - DG Joining DG - DC Joining DC - DC Joining DC - DC Joining DC - DG Joining DG - DC Joining DC - DT Joining DT - DG Joining DG - DG Joining DG - DC Joining DC - DA Joining DA - DT Joining DT - DC Joining DC - DT Joining DT - DG Joining DG - DT Joining DT - DC Joining DC - DC Joining DC - DT Joining DT - DC Joining DC - DT Joining DT - DA Joining DA - DC Joining DC - DT Joining DT - DC Joining DC - DC Joining DC - DC Joining DC - DG Joining DG - DC Joining DC - DA Joining DA - DC Joining DC - DT Joining DT - DG Joining DG - DC Joining DC - DT Joining DT - DC Joining DC - DT Joining DT - DG Joining DG - DT Joining DT - DG Joining DG - DT Joining DT - DC Joining DC - DT Joining DT - DT Joining DT - DC Joining DC - DG Joining DG - DC Joining DC - DT Joining DT - DC Joining DC - DC Joining DC - DT Joining DT - DA Joining DA - DG Joining DG - DT Joining DT - DG Joining DG - DT Joining DT - DC Joining DC - DT Joining DT - DA Joining DA - DG Joining DG - DC Joining DC - DC Joining DC - DC Joining DC - DC Joining DC - DC Joining DC - DG Joining DG - DC Joining DC - DC Joining DC - DT Joining DT - DT Joining DT - DC Joining DC - DA Joining DA - DT Joining DT - DG Joining DG - DG Joining DG - DG Joining DG - DA Joining DA - DC Joining DC - DG Joining DG - DC Joining DC - DC Joining DC - DG Joining DG - DT Joining DT - DC Joining DC - DG Joining DG - DT Joining DT - DA Joining DA - DG Joining DG - DG Joining DG - DG total atoms in file: 4528 Leap added 1808 missing atoms according to residue templates: 1808 H / lone pairs > bond x.1.P x.100.O3' > bond x.10101.P x.10200.O3' > saveamberparm x prmtop prmcrd Checking Unit. WARNING: The unperturbed charge of the unit: -200.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 1164 improper torsions applied Building H-Bond parameters. Marking per-residue atom chain types. (no restraints) > quit Quit