log started: Wed Aug 24 12:26:42 2016 Log file: ./leap.log > # > # ----- leaprc for loading the ff12SB force field > # ----- NOTE: this is designed for PDB format 3! > # Uses frcmod.ff12SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA > # > # 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" } > { "HZ" "H" "sp3" } > { "OH" "O" "sp3" } > { "OS" "O" "sp3" } > { "O" "O" "sp2" } > { "O2" "O" "sp2" } > { "OP" "O" "sp2" } > { "OW" "O" "sp3" } > { "CT" "C" "sp3" } > { "CX" "C" "sp3" } > { "C8" "C" "sp3" } > { "2C" "C" "sp3" } > { "3C" "C" "sp3" } > { "CH" "C" "sp3" } > { "CS" "C" "sp2" } > { "C" "C" "sp2" } > { "CO" "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" } > { "C5" "C" "sp2" } > { "C4" "C" "sp2" } > { "CP" "C" "sp2" } > { "CI" "C" "sp3" } > { "CJ" "C" "sp2" } > { "CW" "C" "sp2" } > { "CV" "C" "sp2" } > { "CR" "C" "sp2" } > { "CA" "C" "sp2" } > { "CY" "C" "sp2" } > { "C0" "Ca" "sp3" } > { "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" } > { "NY" "N" "sp2" } > { "N3" "N" "sp3" } > { "S" "S" "sp3" } > { "SH" "S" "sp3" } > { "P" "P" "sp3" } > { "LP" "" "sp3" } > { "EP" "" "sp3" } > { "F" "F" "sp3" } > { "Cl" "Cl" "sp3" } > { "Br" "Br" "sp3" } > { "I" "I" "sp3" } > { "F-" "F" "sp3" } > { "Cl-" "Cl" "sp3" } > { "Br-" "Br" "sp3" } > { "I-" "I" "sp3" } > { "Li+" "Li" "sp3" } > { "Na+" "Na" "sp3" } > { "K+" "K" "sp3" } > { "Rb+" "Rb" "sp3" } > { "Cs+" "Cs" "sp3" } > { "Mg+" "Mg" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # Load the main parameter set. > # > parm10 = loadamberparams parm10.dat Loading parameters: /opt/AMBER/amber14/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) > frcmod12SB = loadamberparams frcmod.ff12SB Loading parameters: /opt/AMBER/amber14/dat/leap/parm/frcmod.ff12SB Reading force field modification type file (frcmod) Reading title: ff12SB protein backbone and sidechain parameters > # > # Load main chain and terminating amino acid libraries, nucleic acids > # > loadOff amino12.lib Loading library: /opt/AMBER/amber14/dat/leap/lib/amino12.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: HYP 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 aminoct12.lib Loading library: /opt/AMBER/amber14/dat/leap/lib/aminoct12.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: CHYP 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 aminont12.lib Loading library: /opt/AMBER/amber14/dat/leap/lib/aminont12.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 nucleic12.lib Loading library: /opt/AMBER/amber14/dat/leap/lib/nucleic12.lib Loading: A Loading: A3 Loading: A5 Loading: AN Loading: C Loading: C3 Loading: C5 Loading: CN 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: G Loading: G3 Loading: G5 Loading: GN Loading: OHE Loading: U Loading: U3 Loading: U5 Loading: UN > # > # Load water and ions > # > loadOff atomic_ions.lib Loading library: /opt/AMBER/amber14/dat/leap/lib/atomic_ions.lib Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CL Loading: CO Loading: CS Loading: CU Loading: Cl- Loading: Cr Loading: EU Loading: F Loading: FE2 Loading: HG Loading: IOD Loading: K Loading: K+ Loading: LI Loading: MG Loading: MN Loading: NA Loading: NI Loading: Na+ Loading: PB Loading: PD Loading: PT Loading: RB Loading: Ra Loading: SR Loading: Sm Loading: Sn Loading: V2+ Loading: YB2 Loading: ZN > loadOff solvents.lib Loading library: /opt/AMBER/amber14/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: MEOHBOX Loading: NMABOX Loading: OPC Loading: OPCBOX 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: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF > HOH = TP3 > WAT = TP3 > > # > # Define the PDB name map for the amino acids and nucleic acids > # (note: no NHYP! use neutral form for now) > # > addPdbResMap { > { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" } > { 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 "G" "G5" } { 1 "G" "G3" } > { 0 "A" "A5" } { 1 "A" "A3" } > { 0 "C" "C5" } { 1 "C" "C3" } > { 0 "U" "U5" } { 1 "U" "U3" } > { 0 "DG" "DG5" } { 1 "DG" "DG3" } > { 0 "DA" "DA5" } { 1 "DA" "DA3" } > { 0 "DC" "DC5" } { 1 "DC" "DC3" } > { 0 "DT" "DT5" } { 1 "DT" "DT3" } > # some old Amber residue names for RNA: > { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } > { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } > { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } > { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } > # some really old Amber residue names, assuming DNA: > { 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" } > # uncomment out the following if you have this old style RNA files: > # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } > # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } > # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } > # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } > > } > > # try to be good about reading in really old atom names as well: > 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'" } > { "H2*2" "H2''" } > { "HO*2" "HO2'" } > { "H2'1" "H2'" } > { "H2'2" "H2''" } > { "H3*" "H3'" } > { "H4*" "H4'" } > { "H5*1" "H5'" } > { "H5*2" "H5''" } > { "H5'1" "H5'" } > { "H5'2" "H5''" } > { "HO'2" "HO2'" } > { "H5T" "HO5'" } > { "H3T" "HO3'" } > { "O1'" "O4'" } > { "OA" "OP1" } > { "OB" "OP2" } > { "O1P" "OP1" } > { "O2P" "OP2" } > } > > # > # assume that most often proteins use HIE > # > NHIS = NHIE > HIS = HIE > CHIS = CHIE Sourcing: ./act > source leaprc.gaff ----- Source: /opt/AMBER/amber14/dat/leap/cmd/leaprc.gaff ----- Source of /opt/AMBER/amber14/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Wed Aug 24 12:26:44 2016 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "cz" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "no" "N" "sp2" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pc" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "pe" "P" "sp3" } >> { "pf" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff.dat Loading parameters: /opt/AMBER/amber14/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.7, Nov 2013) > > loadamberparams broben.frcmod Loading parameters: ./broben.frcmod Reading force field modification type file (frcmod) Reading title: Bromparms > dibr = loadpdb new.pdb Loading PDB file: ./new.pdb Enter zPdbReadScan from call depth 0. Exit zPdbReadScan from call depth 0. Matching PDB residue names to LEaP variables. (Residue 0: BBZ, Terminal/last, was not found in name map.) Unknown residue: BBZ number: 0 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 1: BBZ, Terminal/last, was not found in name map.) Unknown residue: BBZ number: 1 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 2: BBZ, Terminal/last, was not found in name map.) Unknown residue: BBZ number: 2 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 3: BBZ, Terminal/last, was not found in name map.) Unknown residue: BBZ number: 3 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 4: BBZ, Terminal/last, was not found in name map.) Unknown residue: BBZ number: 4 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 5: BBZ, Terminal/last, was not found in name map.) Unknown residue: BBZ number: 5 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck -no luck (Residue 2515: BBZ, Terminal/last, was not found in name map.) Unknown residue: BBZ number: 2515 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 2516: BBZ, Terminal/last, was not found in name map.) Unknown residue: BBZ number: 2516 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Creating new UNIT for residue: BBZ sequence: 1 Created a new atom named: C1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 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: H7 within residue: .R Created a new atom named: H8 within residue: .R Created a new atom named: H9 within residue: .R Created a new atom named: H10 within residue: .R Created a new atom named: H11 within residue: .R Created a new atom named: Br12 within residue: .R Creating new UNIT for residue: BBZ sequence: 2 Created a new atom named: C1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 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: H7 within residue: .R Created a new atom named: H8 within residue: .R Created a new atom named: H9 within residue: .R Created a new atom named: H10 within residue: .R Created a new atom named: H11 within residue: .R Created a new atom named: Br12 within residue: .R Creating new UNIT for residue: BBZ sequence: 3 Created a new atom named: C1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 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: H7 within residue: .R Created a new atom named: H8 within residue: .R Created a new atom named: H9 within residue: .R Created a new atom named: H10 within residue: .R Created a new atom named: H11 within residue: .R Created a new atom named: Br12 within residue: .R Creating new UNIT for residue: BBZ sequence: 2516 Created a new atom named: C1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 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: H7 within residue: .R Created a new atom named: H8 within residue: .R Created a new atom named: H9 within residue: .R Created a new atom named: H10 within residue: .R Created a new atom named: H11 within residue: .R Created a new atom named: Br12 within residue: .R Creating new UNIT for residue: BBZ sequence: 2517 Created a new atom named: C1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 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: H7 within residue: .R Created a new atom named: H8 within residue: .R Created a new atom named: H9 within residue: .R Created a new atom named: H10 within residue: .R Created a new atom named: H11 within residue: .R Created a new atom named: Br12 within residue: .R total atoms in file: 30204 The file contained 30204 atoms not in residue templates > check dibr Checking 'dibr'.... FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Warning: Close contact of 1.085161 angstroms between .R.A and .R.A Warning: Close contact of 1.476021 angstroms between .R.A and .R.A Warning: Close contact of 1.104693 angstroms between .R.A and .R.A Warning: Close contact of 1.036816 angstroms between .R.A and .R.A Warning: Close contact of 1.488245 angstroms between .R.A and .R.A Warning: Close contact of 1.069378 angstroms between .R.A and .R.A Warning: Close contact of 1.131672 angstroms between .R.A and .R.A Warning: Close contact of 1.031025 angstroms between .R.A and .R.A Warning: Close contact of 1.088252 angstroms between .R.A and .R.A Warning: Close contact of 1.498348 angstroms between .R.A and .R.A Warning: Close contact of 1.134780 angstroms between .R.A and .R.A Warning: Close contact of 1.030451 angstroms between .R.A and .R.A Warning: Close contact of 1.130929 angstroms between .R.A and .R.A Warning: Close contact of 1.485006 angstroms between .R.A and .R.A Warning: Close contact of 1.075393 angstroms between .R.A and .R.A Warning: Close contact of 1.087049 angstroms between .R.A and .R.A Checking parameters for unit 'dibr'. Checking for bond parameters. Checking for angle parameters. check: Errors: 30204 Warnings: 15423 > saveamberparm dibr box.prmtop box.inpcrd Checking Unit. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. > quit Quit