log started: Mon Jul 27 21:15:16 2020 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff19SB 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" } >> { "XC" "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. >> # >> set default cmap on >> parm19 = loadamberparams parm19.dat Loading parameters: /home/packages/amber20/dat/leap/parm/parm19.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod19SB = loadamberparams frcmod.ff19SB Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ff19SB Reading force field modification type file (frcmod) Reading title: ff19SB AA-specific backbone CMAPs for protein 07/25/2019 >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino19.lib Loading library: /home/packages/amber20/dat/leap/lib/amino19.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/packages/amber20/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/packages/amber20/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" "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" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.water.opc ----- Source: /home/packages/amber20/dat/leap/cmd/leaprc.water.opc ----- Source of /home/packages/amber20/dat/leap/cmd/leaprc.water.opc done >> # >> # Load water and ions for OPC + Joung-Chetham monovalent ions for >> # tip4pew + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # for tip4pew >> # >> addAtomTypes { >> { "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" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> { "OW" "O" "sp3" } >> { "HW" "H" "sp3" } >> { "EP" "" "sp3" } >> } >> loadOff atomic_ions.lib Loading library: /home/packages/amber20/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: /home/packages/amber20/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 = OPC >> WAT = OPC >> loadAmberParams frcmod.opc Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.opc Reading force field modification type file (frcmod) Reading title: Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) (UNKNOWN ATOM TYPE: EP) >> loadAmberParams frcmod.ionsjc_tip4pew Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ionsjc_tip4pew Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip4pew Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ions234lm_126_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 normal usage set) >> > > loadamberparams frcmod.ions1lm_126_hfe_opc Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ions1lm_126_hfe_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 HFE set) > ramp=loadpdb RAMP1.pdb Loading PDB file: ./RAMP1.pdb Matching PDB residue names to LEaP variables. Mapped residue CYX, term: Terminal/beginning, seq. number: 0 to: NCYX. Mapped residue SER, term: Terminal/last, seq. number: 80 to: CSER. Added missing heavy atom: .R.A Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC total atoms in file: 683 Leap added 674 missing atoms according to residue templates: 1 Heavy 673 H / lone pairs > bond ramp.27.SG ramp.82.SG > bond ramp.40.SG ramp.72.SG > bond ramp.57.SG ramp.104.SG > SaveAmberParm ramp RAMP1_gas.prmtop RAMP1_gas.inpcrd Checking Unit. /home/packages/amber20/bin/teLeap: Warning! The unperturbed charge of the unit (-2.000000) is not zero. /home/packages/amber20/bin/teLeap: Note. Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 303 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 CSER 1 NCYX 1 WAT 17 ) (no restraints) > addIons ramp Na+ 2 Adding 2 counter ions to "ramp" using 1A grid Total solute charge: -2.00 Max atom radius: 1.98 Grid extends from solute vdw + 1.43 to 7.41 Box: enclosing: -11.23 -9.24 9.20 46.33 40.45 53.17 sized: 52.77 54.76 73.20 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 Volume = 11.02% of box, grid points 28876 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (No solvent overlap) Placed Na+ in ramp at (5.77, 35.76, 38.20). (No solvent overlap) Placed Na+ in ramp at (17.77, 9.76, 43.20). Done adding ions. > solvateOct ramp OPCBOX 10.0 Scaling up box by a factor of 1.413369 to meet diagonal cut criterion Solute vdw bounding box: 45.400 31.108 30.346 Total bounding box for atom centers: 73.667 73.667 73.667 (box expansion for 'iso' is 55.9%) Solvent unit box: 18.865 18.478 19.006 The number of boxes: x= 4 y= 4 z= 4 Volume: 208141.839 A^3 (oct) Total mass 110188.212 amu, Density 0.879 g/cc Added 5569 residues. > addIonsRand ramp NA 19 CL 19 Adding 38 counter ions to "ramp". 5548 solvent molecules will remain. 0: Placed NA in ramp at (13.59, -22.00, 12.19). Placed CL in ramp at (-25.31, 22.35, 13.43). 0: Placed NA in ramp at (-4.36, -17.91, -16.27). Placed CL in ramp at (24.64, 9.57, -8.70). 0: Placed NA in ramp at (24.82, -7.54, 5.20). Placed CL in ramp at (-10.26, -36.41, -11.52). 0: Placed NA in ramp at (27.16, -13.67, -7.61). Placed CL in ramp at (-23.47, 9.75, -21.62). 0: Placed NA in ramp at (14.84, -18.06, -26.65). Placed CL in ramp at (-17.51, 2.76, 31.15). 0: Placed NA in ramp at (-11.93, -31.63, 7.00). Placed CL in ramp at (-7.56, 26.73, 15.67). 0: Placed NA in ramp at (-19.67, -18.08, 18.33). Placed CL in ramp at (-22.24, 5.14, -27.92). 0: Placed NA in ramp at (19.69, -26.15, 1.50). Placed CL in ramp at (28.60, -18.64, -12.80). 0: Placed NA in ramp at (-4.90, 13.74, -19.90). Placed CL in ramp at (-2.70, 19.93, -12.53). 0: Placed NA in ramp at (-6.44, -27.57, -7.72). Placed CL in ramp at (-6.54, -23.80, -19.76). 0: Placed NA in ramp at (-22.09, 14.29, -9.36). Placed CL in ramp at (-0.29, 25.36, 12.12). 0: Placed NA in ramp at (-8.51, 0.60, -27.93). Placed CL in ramp at (-13.51, 4.81, -34.09). 0: Placed NA in ramp at (23.26, -2.28, -12.50). Placed CL in ramp at (8.52, -22.91, 7.93). 0: Placed NA in ramp at (-1.46, -17.10, 11.88). Placed CL in ramp at (28.13, -8.62, 4.11). 0: Placed NA in ramp at (-18.87, 16.62, -8.37). Placed CL in ramp at (-28.37, -10.79, -13.85). 0: Placed NA in ramp at (14.80, -25.02, 13.89). Placed CL in ramp at (-20.89, 11.33, 7.92). 0: Placed NA in ramp at (26.23, 14.49, -17.17). Placed CL in ramp at (-10.60, -21.74, -19.66). 0: Placed NA in ramp at (15.55, -16.14, 19.98). Placed CL in ramp at (23.33, 25.98, 10.70). 0: Placed NA in ramp at (3.19, -20.16, 21.52). Placed CL in ramp at (26.21, -23.69, 6.92). > SaveAmberParm ramp RAMP1_ion.prmtop RAMP1_ion.inpcrd Checking Unit. /home/packages/amber20/bin/teLeap: Note. Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 303 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 CSER 1 NCYX 1 WAT 17 ) (no restraints) > > quit Quit Exiting LEaP: Errors = 0; Warnings = 1; Notes = 2. log started: Mon Jul 27 21:22:49 2020 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff19SB 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" } >> { "XC" "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. >> # >> set default cmap on >> parm19 = loadamberparams parm19.dat Loading parameters: /home/packages/amber20/dat/leap/parm/parm19.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod19SB = loadamberparams frcmod.ff19SB Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ff19SB Reading force field modification type file (frcmod) Reading title: ff19SB AA-specific backbone CMAPs for protein 07/25/2019 >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino19.lib Loading library: /home/packages/amber20/dat/leap/lib/amino19.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/packages/amber20/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/packages/amber20/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" "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" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.water.opc ----- Source: /home/packages/amber20/dat/leap/cmd/leaprc.water.opc ----- Source of /home/packages/amber20/dat/leap/cmd/leaprc.water.opc done >> # >> # Load water and ions for OPC + Joung-Chetham monovalent ions for >> # tip4pew + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # for tip4pew >> # >> addAtomTypes { >> { "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" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> { "OW" "O" "sp3" } >> { "HW" "H" "sp3" } >> { "EP" "" "sp3" } >> } >> loadOff atomic_ions.lib Loading library: /home/packages/amber20/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: /home/packages/amber20/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 = OPC >> WAT = OPC >> loadAmberParams frcmod.opc Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.opc Reading force field modification type file (frcmod) Reading title: Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) (UNKNOWN ATOM TYPE: EP) >> loadAmberParams frcmod.ionsjc_tip4pew Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ionsjc_tip4pew Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip4pew Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ions234lm_126_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 normal usage set) >> > > loadamberparams frcmod.ions1lm_126_hfe_opc Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ions1lm_126_hfe_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 HFE set) > ramp=loadpdb RAMP1.pdb Loading PDB file: ./RAMP1.pdb Matching PDB residue names to LEaP variables. Mapped residue CYX, term: Terminal/beginning, seq. number: 0 to: NCYX. Mapped residue SER, term: Terminal/last, seq. number: 80 to: CSER. Added missing heavy atom: .R.A Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC total atoms in file: 683 Leap added 674 missing atoms according to residue templates: 1 Heavy 673 H / lone pairs > bond ramp.27.SG ramp.82.SG > bond ramp.40.SG ramp.72.SG > bond ramp.57.SG ramp.104.SG > SaveAmberParm ramp RAMP1_gas.prmtop RAMP1_gas.inpcrd Checking Unit. /home/packages/amber20/bin/teLeap: Warning! The unperturbed charge of the unit (-2.000000) is not zero. /home/packages/amber20/bin/teLeap: Note. Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 303 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 CSER 1 NCYX 1 WAT 17 ) (no restraints) > addIons ramp Na+ 2 Adding 2 counter ions to "ramp" using 1A grid Total solute charge: -2.00 Max atom radius: 1.98 Grid extends from solute vdw + 1.43 to 7.41 Box: enclosing: -11.23 -9.24 9.20 46.33 40.45 53.17 sized: 52.77 54.76 73.20 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 Volume = 11.02% of box, grid points 28876 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (No solvent overlap) Placed Na+ in ramp at (5.77, 35.76, 38.20). (No solvent overlap) Placed Na+ in ramp at (17.77, 9.76, 43.20). Done adding ions. > solvateOct ramp OPCBOX 10.0 Scaling up box by a factor of 1.413369 to meet diagonal cut criterion Solute vdw bounding box: 45.400 31.108 30.346 Total bounding box for atom centers: 73.667 73.667 73.667 (box expansion for 'iso' is 55.9%) Solvent unit box: 18.865 18.478 19.006 The number of boxes: x= 4 y= 4 z= 4 Volume: 208141.839 A^3 (oct) Total mass 110188.212 amu, Density 0.879 g/cc Added 5569 residues. > addIonsRand ramp Na+ 19 Cl- 19 Adding 38 counter ions to "ramp". 5548 solvent molecules will remain. 0: Placed Na+ in ramp at (-7.08, -7.93, -18.84). Placed Cl- in ramp at (-25.85, -12.94, 1.30). 0: Placed Na+ in ramp at (11.05, -29.23, -9.68). Placed Cl- in ramp at (-16.48, -19.37, -18.30). 0: Placed Na+ in ramp at (-28.24, -1.82, 14.52). Placed Cl- in ramp at (4.43, -24.51, -20.30). 0: Placed Na+ in ramp at (-0.51, 25.51, -14.29). Placed Cl- in ramp at (11.73, 34.82, -5.15). 0: Placed Na+ in ramp at (24.47, -0.05, 11.53). Placed Cl- in ramp at (-13.82, 11.61, -23.45). 0: Placed Na+ in ramp at (-4.43, -14.63, -19.95). Placed Cl- in ramp at (17.53, -25.12, 13.50). 0: Placed Na+ in ramp at (4.37, 6.67, -30.51). Placed Cl- in ramp at (4.70, 21.42, 13.96). 0: Placed Na+ in ramp at (3.51, -28.36, -13.89). Placed Cl- in ramp at (-8.12, -28.47, 2.24). 0: Placed Na+ in ramp at (-4.16, -1.08, 26.61). Placed Cl- in ramp at (-7.56, -7.20, 19.85). 0: Placed Na+ in ramp at (0.48, -27.92, -11.49). Placed Cl- in ramp at (-16.24, 16.52, 14.58). 0: Placed Na+ in ramp at (13.72, -4.33, -31.29). Placed Cl- in ramp at (-5.42, 25.25, 1.45). 0: Placed Na+ in ramp at (-4.76, 5.51, 20.48). Placed Cl- in ramp at (26.11, 20.52, -13.58). 0: Placed Na+ in ramp at (15.67, 5.42, -0.80). Placed Cl- in ramp at (0.52, -11.59, 21.60). 0: Placed Na+ in ramp at (-14.92, -2.17, -0.11). Placed Cl- in ramp at (19.04, -17.19, -7.15). 0: Placed Na+ in ramp at (-12.99, 14.79, -23.72). Placed Cl- in ramp at (-20.54, 17.41, 1.28). 0: Placed Na+ in ramp at (13.88, 30.71, 11.26). Placed Cl- in ramp at (-5.28, -17.40, -18.99). 0: Placed Na+ in ramp at (24.55, 9.19, 5.25). Placed Cl- in ramp at (-8.19, 29.18, -2.92). 0: Placed Na+ in ramp at (14.64, 16.01, 12.20). Placed Cl- in ramp at (18.57, -23.58, 1.68). 0: Placed Na+ in ramp at (6.49, -16.59, 17.17). Placed Cl- in ramp at (26.73, 1.90, -2.11). > SaveAmberParm ramp RAMP1_ion.prmtop RAMP1_ion.inpcrd Checking Unit. /home/packages/amber20/bin/teLeap: Note. Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 303 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 CSER 1 NCYX 1 WAT 17 ) (no restraints) > > quit Quit Exiting LEaP: Errors = 0; Warnings = 1; Notes = 2. log started: Fri Sep 18 14:59:17 2020 Log file: ./leap.log >>> # >>> # ----- leaprc for loading the ff19SB 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" } >>> { "XC" "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. >>> # >>> set default cmap on >>> parm19 = loadamberparams parm19.dat Loading parameters: /home/packages/amber20/dat/leap/parm/parm19.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >>> frcmod19SB = loadamberparams frcmod.ff19SB Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ff19SB Reading force field modification type file (frcmod) Reading title: ff19SB AA-specific backbone CMAPs for protein 07/25/2019 >>> # >>> # Load main chain and terminating amino acid libraries >>> # >>> loadOff amino19.lib Loading library: /home/packages/amber20/dat/leap/lib/amino19.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/packages/amber20/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/packages/amber20/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" "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" } >>> } >>> >>> # >>> # assume that most often proteins use HIE >>> # >>> NHIS = NHIE >>> HIS = HIE >>> CHIS = CHIE >> >> source leaprc.water.opc ----- Source: /home/packages/amber20/dat/leap/cmd/leaprc.water.opc ----- Source of /home/packages/amber20/dat/leap/cmd/leaprc.water.opc done >>> # >>> # Load water and ions for OPC + Joung-Chetham monovalent ions for >>> # tip4pew + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >>> # for tip4pew >>> # >>> addAtomTypes { >>> { "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" } >>> { "Tl+" "Tl" "sp3" } >>> { "Cu+" "Cu" "sp3" } >>> { "Ag+" "Ag" "sp3" } >>> { "Be2+" "Be" "sp3" } >>> { "Cu2+" "Cu" "sp3" } >>> { "Ni2+" "Ni" "sp3" } >>> { "Pt2+" "Pt" "sp3" } >>> { "Zn2+" "Zn" "sp3" } >>> { "Co2+" "Co" "sp3" } >>> { "Pd2+" "Pd" "sp3" } >>> { "Ag2+" "Ag" "sp3" } >>> { "Cr2+" "Cr" "sp3" } >>> { "Fe2+" "Fe" "sp3" } >>> { "Mg2+" "Mg" "sp3" } >>> { "V2+" "V" "sp3" } >>> { "Mn2+" "Mn" "sp3" } >>> { "Hg2+" "Hg" "sp3" } >>> { "Cd2+" "Cd" "sp3" } >>> { "Yb2+" "Yb" "sp3" } >>> { "Ca2+" "Ca" "sp3" } >>> { "Sn2+" "Sn" "sp3" } >>> { "Pb2+" "Pb" "sp3" } >>> { "Eu2+" "Eu" "sp3" } >>> { "Sr2+" "Sr" "sp3" } >>> { "Sm2+" "Sm" "sp3" } >>> { "Ba2+" "Ba" "sp3" } >>> { "Ra2+" "Ra" "sp3" } >>> { "Al3+" "Al" "sp3" } >>> { "Fe3+" "Fe" "sp3" } >>> { "Cr3+" "Cr" "sp3" } >>> { "In3+" "In" "sp3" } >>> { "Tl3+" "Tl" "sp3" } >>> { "Y3+" "Y" "sp3" } >>> { "La3+" "La" "sp3" } >>> { "Ce3+" "Ce" "sp3" } >>> { "Pr3+" "Pr" "sp3" } >>> { "Nd3+" "Nd" "sp3" } >>> { "Sm3+" "Sm" "sp3" } >>> { "Eu3+" "Eu" "sp3" } >>> { "Gd3+" "Gd" "sp3" } >>> { "Tb3+" "Tb" "sp3" } >>> { "Dy3+" "Dy" "sp3" } >>> { "Er3+" "Er" "sp3" } >>> { "Tm3+" "Tm" "sp3" } >>> { "Lu3+" "Lu" "sp3" } >>> { "Hf4+" "Hf" "sp3" } >>> { "Zr4+" "Zr" "sp3" } >>> { "Ce4+" "Ce" "sp3" } >>> { "U4+" "U" "sp3" } >>> { "Pu4+" "Pu" "sp3" } >>> { "Th4+" "Th" "sp3" } >>> { "OW" "O" "sp3" } >>> { "HW" "H" "sp3" } >>> { "EP" "" "sp3" } >>> } >>> loadOff atomic_ions.lib Loading library: /home/packages/amber20/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: /home/packages/amber20/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 = OPC >>> WAT = OPC >>> loadAmberParams frcmod.opc Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.opc Reading force field modification type file (frcmod) Reading title: Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) (UNKNOWN ATOM TYPE: EP) >>> loadAmberParams frcmod.ionsjc_tip4pew Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ionsjc_tip4pew Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008) >>> loadAmberParams frcmod.ions234lm_126_tip4pew Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ions234lm_126_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 normal usage set) >>> >> >> loadamberparams frcmod.ions1lm_126_hfe_opc Loading parameters: /home/packages/amber20/dat/leap/parm/frcmod.ions1lm_126_hfe_opc Reading force field modification type file (frcmod) Reading title: Li/Merz monovalent ion parameters for OPC water model (12-6 HFE set) >> ramp=loadpdb RAMP1.pdb Loading PDB file: ./RAMP1.pdb Matching PDB residue names to LEaP variables. Mapped residue CYX, term: Terminal/beginning, seq. number: 0 to: NCYX. Mapped residue SER, term: Terminal/last, seq. number: 80 to: CSER. Added missing heavy atom: .R.A Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC total atoms in file: 683 Leap added 674 missing atoms according to residue templates: 1 Heavy 673 H / lone pairs >> bond ramp.27.SG ramp.82.SG >> bond ramp.40.SG ramp.72.SG >> bond ramp.57.SG ramp.104.SG >> SaveAmberParm ramp RAMP1_gas.prmtop RAMP1_gas.inpcrd Checking Unit. /home/packages/amber20/bin/teLeap: Warning! The unperturbed charge of the unit (-2.000000) is not zero. /home/packages/amber20/bin/teLeap: Note. Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 303 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 CSER 1 NCYX 1 WAT 17 ) (no restraints) >> addIons ramp Na+ 2 Adding 2 counter ions to "ramp" using 1A grid Total solute charge: -2.00 Max atom radius: 1.98 Grid extends from solute vdw + 1.43 to 7.41 Box: enclosing: -11.23 -9.24 9.20 46.33 40.45 53.17 sized: 52.77 54.76 73.20 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 Volume = 11.02% of box, grid points 28876 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (No solvent overlap) Placed Na+ in ramp at (5.77, 35.76, 38.20). (No solvent overlap) Placed Na+ in ramp at (17.77, 9.76, 43.20). Done adding ions. >> solvateOct ramp OPCBOX 10.0 Scaling up box by a factor of 1.413369 to meet diagonal cut criterion Solute vdw bounding box: 45.400 31.108 30.346 Total bounding box for atom centers: 73.667 73.667 73.667 (box expansion for 'iso' is 55.9%) Solvent unit box: 18.865 18.478 19.006 The number of boxes: x= 4 y= 4 z= 4 Volume: 208141.839 A^3 (oct) Total mass 110188.212 amu, Density 0.879 g/cc Added 5569 residues. >> addIonsRand ramp Na+ 19 Cl- 19 Adding 38 counter ions to "ramp". 5548 solvent molecules will remain. 0: Placed Na+ in ramp at (-23.37, 7.04, -13.48). Placed Cl- in ramp at (-5.59, -27.07, -4.96). 0: Placed Na+ in ramp at (2.04, 20.43, -1.27). Placed Cl- in ramp at (-19.91, 13.96, -19.00). 0: Placed Na+ in ramp at (-9.65, 9.71, 14.61). Placed Cl- in ramp at (-15.34, 21.12, 19.57). 0: Placed Na+ in ramp at (15.48, -16.93, 5.85). Placed Cl- in ramp at (10.17, -11.30, 36.17). 0: Placed Na+ in ramp at (19.57, 15.83, -5.41). Placed Cl- in ramp at (26.46, 14.33, 9.24). 0: Placed Na+ in ramp at (29.03, 23.31, 7.66). Placed Cl- in ramp at (10.37, 24.64, 18.25). 0: Placed Na+ in ramp at (4.53, -12.05, -7.72). Placed Cl- in ramp at (-22.43, -0.75, 18.32). 0: Placed Na+ in ramp at (8.30, 27.56, -9.47). Placed Cl- in ramp at (4.54, 31.57, 15.34). 0: Placed Na+ in ramp at (9.58, -23.38, -20.88). Placed Cl- in ramp at (-0.68, -10.10, -27.65). 0: Placed Na+ in ramp at (9.17, 7.31, -17.19). Placed Cl- in ramp at (18.61, -16.18, -10.62). 0: Placed Na+ in ramp at (-16.66, 23.82, 13.72). Placed Cl- in ramp at (-23.81, -7.67, 14.99). 0: Placed Na+ in ramp at (25.96, -3.00, -3.03). Placed Cl- in ramp at (-10.76, -21.97, -0.75). 0: Placed Na+ in ramp at (-9.24, 13.20, 17.46). Placed Cl- in ramp at (11.68, -12.56, 14.92). 0: Placed Na+ in ramp at (5.42, -18.09, 21.46). Placed Cl- in ramp at (22.01, -19.01, -17.94). 0: Placed Na+ in ramp at (-8.11, 9.45, -35.38). Placed Cl- in ramp at (28.87, -3.37, -3.79). 0: Placed Na+ in ramp at (18.48, -12.07, -23.70). Placed Cl- in ramp at (29.83, 20.21, -12.26). 0: Placed Na+ in ramp at (15.17, 4.71, 15.73). Placed Cl- in ramp at (-28.30, 8.23, 2.00). 0: Placed Na+ in ramp at (18.42, 1.78, 3.84). Placed Cl- in ramp at (-18.19, 5.15, 21.10). 0: Placed Na+ in ramp at (10.43, -17.96, 12.09). Placed Cl- in ramp at (-18.74, 7.22, 24.33). >> SaveAmberParm ramp RAMP1_ion.prmtop RAMP1_ion.inpcrd Checking Unit. /home/packages/amber20/bin/teLeap: Note. Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 303 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 CSER 1 NCYX 1 WAT 17 ) (no restraints) >> > > quit Quit Exiting LEaP: Errors = 0; Warnings = 1; Notes = 2.