log started: Tue Aug 24 14:45:22 2021 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed 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" } >> { "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" } >> } >> # >> # Load the main parameter set. >> # >> parm10 = loadamberparams parm10.dat Loading parameters: /home/ipsita/Downloads/amber20_src/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /home/ipsita/Downloads/amber20_src/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino12.lib Loading library: /home/ipsita/Downloads/amber20_src/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: /home/ipsita/Downloads/amber20_src/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: /home/ipsita/Downloads/amber20_src/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 >> >> # >> # Define the PDB name map for the amino acids >> # >> 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" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.gaff ----- Source: /home/ipsita/Downloads/amber20_src/dat/leap/cmd/leaprc.gaff ----- Source of /home/ipsita/Downloads/amber20_src/dat/leap/cmd/leaprc.gaff done >> logFile leap.log log started: Tue Aug 24 14:45:22 2021 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" } >> { "op" "O" "sp3" } >> { "oq" "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" } >> { "ni" "N" "sp2" } >> { "nj" "N" "sp2" } >> { "nk" "N" "sp3" } >> { "nl" "N" "sp3" } >> { "nm" "N" "sp2" } >> { "nn" "N" "sp2" } >> { "no" "N" "sp2" } >> { "np" "N" "sp3" } >> { "nq" "N" "sp3" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "sp" "S" "sp3" } >> { "sq" "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: /home/ipsita/Downloads/amber20_src/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > set default PBRadii mbondi3 Using ArgH and AspGluO modified Bondi2 radii > loadAmberPrep cyl.prepin Loading Prep file: ./cyl.prepin Loaded UNIT: CYL > loadAmberParams frcmod.cyl Loading parameters: ./frcmod.cyl Reading force field modification type file (frcmod) Reading title: Remark line goes here > #loadAmberParams frcmod1.cyl > x = loadPDB comp.pdb Loading PDB file: ./comp.pdb Matching PDB residue names to LEaP variables. Mapped residue LEU, term: Terminal/beginning, seq. number: 0 to: NLEU. Mapped residue HIE, term: Terminal/last, seq. number: 160 to: CHIE. Added missing heavy atom: .R.A total atoms in file: 1305 Leap added 1312 missing atoms according to residue templates: 1 Heavy 1311 H / lone pairs > saveAmberParm x gfp.parm7 gfp.rst7 Checking Unit. /home/ipsita/Downloads/amber20_src/bin/teLeap: Warning! There is a bond of 3.643 angstroms between C16 and F2 atoms: ------- .R.A and .R.A /home/ipsita/Downloads/amber20_src/bin/teLeap: Warning! There is a bond of 3.554 angstroms between C15 and F1 atoms: ------- .R.A and .R.A /home/ipsita/Downloads/amber20_src/bin/teLeap: Warning! There is a bond of 4.824 angstroms between C15 and O3 atoms: ------- .R.A and .R.A /home/ipsita/Downloads/amber20_src/bin/teLeap: Warning! There is a bond of 4.498 angstroms between C11 and C6 atoms: ------- .R.A and .R.A /home/ipsita/Downloads/amber20_src/bin/teLeap: Warning! There is a bond of 8.622 angstroms between C11 and C18 atoms: ------- .R.A and .R.A /home/ipsita/Downloads/amber20_src/bin/teLeap: Warning! There is a bond of 7.548 angstroms between C9 and C atoms: ------- .R.A and .R.A /home/ipsita/Downloads/amber20_src/bin/teLeap: Warning! The unperturbed charge of the unit (-8.999998) is not zero. /home/ipsita/Downloads/amber20_src/bin/teLeap: Note. Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find bond parameter for: os - hx /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find bond parameter for: n4 - hx /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find bond parameter for: os - hc Building angle parameters. /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: C - N - C /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: os - n4 - hx /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: o - n4 - hx /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: n4 - c3 - h1 /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: n4 - c3 - h1 /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: n4 - os - hx /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: c3 - n4 - hx /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: hc - c3 - h1 /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: c3 - os - hc /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: c3 - C - N /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: C - c3 - ss /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! Could not find angle parameter: N - C - c3 Building proper torsion parameters. /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! ** No torsion terms for c3-c3-C-N /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! ** No torsion terms for c3-c3-C-N /home/ipsita/Downloads/amber20_src/bin/teLeap: Error! ** No torsion terms for N-C-c3-ss Building improper torsion parameters. old PREP-specified impropers: total 462 improper torsions applied 0 improper torsions in old prep form Building H-Bond parameters. Incorporating Non-Bonded adjustments. /home/ipsita/Downloads/amber20_src/bin/teLeap: Warning! Parameter file was not saved. > quit Quit Exiting LEaP: Errors = 18; Warnings = 8; Notes = 1.