log started: Mon Sep 7 12:01:02 2020 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: /cm/shared/apps/Amber18-MPI-Update-14.01.2020/amber18/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) > > source leaprc.protein.ff14SB ----- Source: /cm/shared/apps/Amber18-MPI-Update-14.01.2020/amber18/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /cm/shared/apps/Amber18-MPI-Update-14.01.2020/amber18/dat/leap/cmd/leaprc.protein.ff14SB done >> logFile leap.log log started: Mon Sep 7 12:01:09 2020 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: /cm/shared/apps/Amber18-MPI-Update-14.01.2020/amber18/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /cm/shared/apps/Amber18-MPI-Update-14.01.2020/amber18/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: /cm/shared/apps/Amber18-MPI-Update-14.01.2020/amber18/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: /cm/shared/apps/Amber18-MPI-Update-14.01.2020/amber18/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: /cm/shared/apps/Amber18-MPI-Update-14.01.2020/amber18/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 > > set default PBRadii mbondi3 Using ArgH and AspGluO modified Bondi2 radii > HAR = loadMol2 HAR.mol2 Loading Mol2 file: ./HAR.mol2 Reading MOLECULE named HAR > HAR = loadAmberParams HAR.frcmod Loading parameters: ./HAR.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > list ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHID CHIE CHIP CHIS CHYP CILE CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX GLH GLN GLU GLY HAR HID HIE HIP HIS HYP ILE LEU LYN LYS MET NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL PHE PRO SER THR TRP TYR VAL frcmod14SBgaff parm10 > saveOff HAR HAR.lib Saving HAR. > loadOff HAR.lib Loading library: ./HAR.lib Loading: HAR > list ACE ALA ARG ASH ASN ASP CALA CARG CASN CASP CCYS CCYX CGLN CGLU CGLY CHID CHIE CHIP CHIS CHYP CILE CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM CYS CYX GLH GLN GLU GLY HAR HID HIE HIP HIS HYP ILE LEU LYN LYS MET NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE NHIP NHIS NILE NLEU NLYS NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL PHE PRO SER THR TRP TYR VAL frcmod14SBgaff parm10 > desc HAR.1.N STRING (with no reference): 'HAR.1.N' > desc HAR.1.C STRING (with no reference): 'HAR.1.C' > desc HAR.1.N2 STRING (with no reference): 'HAR.1.N2' > desc HAR PARMSET --Atoms NT Mass= 14.01 Polar= 0.53 E = 0.17 R= 1.82 Element=N Hybrid= Sp3 Desc: N2 Mass= 14.01 Polar= 0.53 E = 0.17 R= 1.82 Element=N Hybrid= Sp2 Desc: CT Mass= 12.01 Polar= 0.88 E = 0.11 R= 1.91 Element=C Hybrid= Sp3 Desc: C Mass= 12.01 Polar= 0.62 E = 0.09 R= 1.91 Element=C Hybrid= Sp2 Desc: CM Mass= 12.01 Polar= 0.36 E = 0.09 R= 1.91 Element=C Hybrid= Sp2 Desc: O Mass= 16.00 Polar= 0.43 E = 0.21 R= 1.66 Element=O Hybrid= Sp2 Desc: OH Mass= 16.00 Polar= 0.47 E = 0.21 R= 1.72 Element=O Hybrid= Sp3 Desc: H Mass= 1.01 Polar= 0.16 E = 0.02 R= 0.60 Element=H Hybrid= Sp3 Desc: H1 Mass= 1.01 Polar= 0.14 E = 0.02 R= 1.39 Element=H Hybrid= Sp3 Desc: HC Mass= 1.01 Polar= 0.14 E = 0.02 R= 1.49 Element=H Hybrid= Sp3 Desc: HO Mass= 1.01 Polar= 0.14 E = 0.00 R= 0.00 Element=H Hybrid= Sp3 Desc: --Bonds CT - NT Kb= 367.00 R0= 1.47 Desc: H - NT Kb= 434.00 R0= 1.01 Desc: CM - NT Kb= 477.00 R0= 1.34 Desc: NT - OH Kb= 0.00 R0= 0.00 Desc: CM - N2 Kb= 477.00 R0= 1.34 Desc: H - N2 Kb= 434.00 R0= 1.01 Desc: C - CT Kb= 317.00 R0= 1.52 Desc: CT - CT Kb= 310.00 R0= 1.53 Desc: CT - H1 Kb= 340.00 R0= 1.09 Desc: C - O Kb= 570.00 R0= 1.23 Desc: C - OH Kb= 450.00 R0= 1.36 Desc: CT - HC Kb= 340.00 R0= 1.09 Desc: HO - OH Kb= 553.00 R0= 0.96 Desc: --Angles C - CT - NT Kt= 80.00 T0= 111.20 Desc: CT - CT - NT Kt= 80.00 T0= 111.20 Desc: H1 - CT - NT Kt= 50.00 T0= 109.50 Desc: NT - CM - NT Kt= 70.00 T0= 120.00 Desc: N2 - CM - NT Kt= 70.00 T0= 120.00 Desc: HO - OH - NT Kt= 0.00 T0= 0.00 Desc: CT - NT - H Kt= 50.00 T0= 109.50 Desc: CT - C - O Kt= 80.00 T0= 120.40 Desc: CT - C - OH Kt= 80.00 T0= 110.00 Desc: CT - CT - CT Kt= 40.00 T0= 109.50 Desc: CT - CT - HC Kt= 50.00 T0= 109.50 Desc: C - CT - CT Kt= 63.00 T0= 111.10 Desc: C - CT - H1 Kt= 50.00 T0= 109.50 Desc: C - OH - HO Kt= 50.00 T0= 113.00 Desc: CT - CT - H1 Kt= 50.00 T0= 109.50 Desc: CM - NT - CT Kt= 0.00 T0= 0.00 Desc: CM - NT - H Kt= 0.00 T0= 0.00 Desc: CM - NT - OH Kt= 0.00 T0= 0.00 Desc: CM - N2 - H Kt= 50.00 T0= 120.00 Desc: O - C - OH Kt= 80.00 T0= 120.00 Desc: H - NT - OH Kt= 0.00 T0= 0.00 Desc: H - NT - H Kt= 35.00 T0= 109.50 Desc: HC - CT - HC Kt= 35.00 T0= 109.50 Desc: H1 - CT - H1 Kt= 35.00 T0= 109.50 Desc: --Torsions NT - CT - C - O Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc: NT - CT - C - OH Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc: CT - CT - CT - NT Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc: HC - CT - CT - NT Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc: NT - CM - NT - OH Kp= 1.52 N=2 P0= 180.00 Order: 0123 Desc: H - NT - CM - NT Kp= 1.52 N=2 P0= 180.00 Order: 0123 Desc: H - N2 - CM - NT Kp= 2.40 N=2 P0= 180.00 Order: 0123 Desc: CT - NT - CM - NT Kp= 1.52 N=2 P0= 180.00 Order: 0123 Desc: CT - NT - CM - N2 Kp= 1.52 N=2 P0= 180.00 Order: 0123 Desc: H - NT - CM - N2 Kp= 1.52 N=2 P0= 180.00 Order: 0123 Desc: N2 - CM - NT - OH Kp= 1.52 N=2 P0= 180.00 Order: 0123 Desc: CT - C - OH - HO Kp= 2.30 N=2 P0= 180.00 Order: 0123 Desc: CT - CT - CT - CT Kp= 0.18 N=3 P0= 0.00 Order: 0123 Desc: CT - CT - CT - CT Kp= 0.25 N=2 P0= 180.00 Order: 0123 Desc: CT - CT - CT - CT Kp= 0.20 N=1 P0= 180.00 Order: 0123 Desc: CT - CT - CT - HC Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc: C - CT - NT - H Kp= 0.30 N=3 P0= 0.00 Order: 0123 Desc: C - CT - CT - CT Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc: C - CT - CT - HC Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc: CT - CT - NT - H Kp= 0.30 N=3 P0= 0.00 Order: 0123 Desc: CT - CT - C - O Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc: CT - CT - C - OH Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc: CT - CT - CT - H1 Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc: CM - NT - CT - CT Kp= 0.30 N=3 P0= 0.00 Order: 0123 Desc: CM - NT - CT - H1 Kp= 0.30 N=3 P0= 0.00 Order: 0123 Desc: CM - NT - OH - HO Kp= 0.00 N=0 P0= 0.00 Order: 0123 Desc: H1 - CT - C - O Kp= 0.80 N=1 P0= 0.00 Order: 0123 Desc: H1 - CT - C - O Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc: H1 - CT - C - O Kp= 0.08 N=3 P0= 180.00 Order: 0123 Desc: HO - OH - C - O Kp= 2.30 N=2 P0= 180.00 Order: 0123 Desc: HO - OH - C - O Kp= 1.90 N=1 P0= 0.00 Order: 0123 Desc: H1 - CT - C - OH Kp= 0.00 N=2 P0= 0.00 Order: 0123 Desc: H - NT - CT - H1 Kp= 0.30 N=3 P0= 0.00 Order: 0123 Desc: H1 - CT - CT - HC Kp= 0.16 N=3 P0= 0.00 Order: 0123 Desc: HC - CT - CT - HC Kp= 0.15 N=3 P0= 0.00 Order: 0123 Desc: H - NT - OH - HO Kp= 0.00 N=0 P0= 0.00 Order: 0123 Desc: --Impropers CT - O - C - OH Kp= 10.50 N=2 P0= 180.00 Order: 0123 Desc: N2 - NT - CM - NT Kp= 1.10 N=2 P0= 180.00 Order: 0123 Desc: --HBonds --None --Nonbonded Edits --None > quit Quit Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.