log started: Fri Dec 14 13:35:47 2018 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff14SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # Uses frcmod.ff14SB 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: /usr/local/amber18/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /usr/local/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, nucleic acids >> # >> loadOff amino12.lib Loading library: /usr/local/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: /usr/local/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: /usr/local/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 >> loadOff nucleic12.lib Loading library: /usr/local/amber18/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: /usr/local/amber18/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /usr/local/amber18/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX 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 >> # >> addPdbResMap { >> { 0 "HYP" "NHYP" } { 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 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" } >> >> } >> >> # 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''" } >> { "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 >> > > #Load the PDBs > cha-cat =loadpdb cha-cat_moe.pdb Loading PDB file: ./cha-cat_moe.pdb Matching PDB residue names to LEaP variables. Mapped residue GLU, term: Terminal/beginning, seq. number: 0 to: NGLU. Mapped residue VAL, term: Terminal/last, seq. number: 220 to: CVAL. Mapped residue SER, term: Terminal/beginning, seq. number: 221 to: NSER. Mapped residue ASN, term: Terminal/last, seq. number: 329 to: CASN. total atoms in file: 4946 > > solvatebox cha-cat TIP3PBOX 12 Solute vdw bounding box: 76.689 43.131 56.763 Total bounding box for atom centers: 100.689 67.131 80.763 Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 6 y= 4 z= 5 Total vdw box size: 103.257 69.842 83.804 angstroms. Volume: 604361.944 A^3 Total mass 305322.364 amu, Density 0.839 g/cc Added 14938 residues. > > loadamberparams frcmod.ionsjc_tip3p Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) > loadamberparams frcmod.ions234lm_hfe_tip3p Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.ions234lm_hfe_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 HFE set) (UNKNOWN ATOM TYPE: Be2+) (UNKNOWN ATOM TYPE: Cu2+) (UNKNOWN ATOM TYPE: Ni2+) (UNKNOWN ATOM TYPE: Pt2+) (UNKNOWN ATOM TYPE: Zn2+) (UNKNOWN ATOM TYPE: Co2+) (UNKNOWN ATOM TYPE: Pd2+) (UNKNOWN ATOM TYPE: Ag2+) (UNKNOWN ATOM TYPE: Cr2+) (UNKNOWN ATOM TYPE: Fe2+) (UNKNOWN ATOM TYPE: Mg2+) (UNKNOWN ATOM TYPE: V2+) (UNKNOWN ATOM TYPE: Mn2+) (UNKNOWN ATOM TYPE: Hg2+) (UNKNOWN ATOM TYPE: Cd2+) (UNKNOWN ATOM TYPE: Yb2+) (UNKNOWN ATOM TYPE: Ca2+) (UNKNOWN ATOM TYPE: Sn2+) (UNKNOWN ATOM TYPE: Pb2+) (UNKNOWN ATOM TYPE: Eu2+) (UNKNOWN ATOM TYPE: Sr2+) (UNKNOWN ATOM TYPE: Sm2+) (UNKNOWN ATOM TYPE: Ba2+) (UNKNOWN ATOM TYPE: Ra2+) (UNKNOWN ATOM TYPE: Al3+) (UNKNOWN ATOM TYPE: Fe3+) (UNKNOWN ATOM TYPE: Cr3+) (UNKNOWN ATOM TYPE: In3+) (UNKNOWN ATOM TYPE: Tl3+) (UNKNOWN ATOM TYPE: Y3+) (UNKNOWN ATOM TYPE: La3+) (UNKNOWN ATOM TYPE: Ce3+) (UNKNOWN ATOM TYPE: Pr3+) (UNKNOWN ATOM TYPE: Nd3+) (UNKNOWN ATOM TYPE: Sm3+) (UNKNOWN ATOM TYPE: Eu3+) (UNKNOWN ATOM TYPE: Gd3+) (UNKNOWN ATOM TYPE: Tb3+) (UNKNOWN ATOM TYPE: Dy3+) (UNKNOWN ATOM TYPE: Er3+) (UNKNOWN ATOM TYPE: Tm3+) (UNKNOWN ATOM TYPE: Lu3+) (UNKNOWN ATOM TYPE: Hf4+) (UNKNOWN ATOM TYPE: Zr4+) (UNKNOWN ATOM TYPE: Ce4+) (UNKNOWN ATOM TYPE: U4+) (UNKNOWN ATOM TYPE: Pu4+) (UNKNOWN ATOM TYPE: Th4+) > > #Make the disulfide bonds > bond cha-cat.23.SG cha-cat.66.SG > bond cha-cat.57.SG cha-cat.99.SG > bond cha-cat.157.SG cha-cat.210.SG > > addIonsRand cha-cat Na+ 0 2 Na+ ions required to neutralize. Adding 2 counter ions to "cha-cat". 14936 solvent molecules will remain. 0: Placed Na+ in cha-cat at (24.62, 23.31, -6.63). 0: Placed Na+ in cha-cat at (38.67, -0.56, -26.24). > > #check cha-cat > > #Save topologies files > saveamberparm cha-cat cha-cat.top cha-cat.crd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1061 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CASN 1 CVAL 1 NGLU 1 NSER 1 WAT 14936 ) (no restraints) > saveamberparm cha-cat cha-cat.prmtop cha-cat.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 1061 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CASN 1 CVAL 1 NGLU 1 NSER 1 WAT 14936 ) (no restraints) > > quit Quit Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.