log started: Wed Mar 23 16:01:44 2022 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/debasish/PROGRAM/amber18/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/debasish/PROGRAM/amber18/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/debasish/PROGRAM/amber18/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/debasish/PROGRAM/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: /home/debasish/PROGRAM/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" "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.tip3p ----- Source: /home/debasish/PROGRAM/amber18/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/debasish/PROGRAM/amber18/dat/leap/cmd/leaprc.water.tip3p done >> # >> # Load water and ions for TIP3P + Li/Merz monovalent ions >> # + Joung-Chetham monovalent ions >> # + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # >> # Note: the Li/Merz monovalent set is loaded only to get Tl+, >> # Cu+, Ag+ NH4+, H3O+. Since we load Joung-Cheatham second, >> # the alkali halide parameters come from the Joung-Cheatham set >> # >> addAtomTypes { >> { "HW" "H" "sp3" } >> { "OW" "O" "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" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "NH4+" "N" "sp3" } >> { "H3O+" "O" "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" } >> } >> loadOff atomic_ions.lib Loading library: /home/debasish/PROGRAM/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: /home/debasish/PROGRAM/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 >> loadAmberParams frcmod.tip3p Loading parameters: /home/debasish/PROGRAM/amber18/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water >> loadAmberParams frcmod.ions1lm_126_tip3p Loading parameters: /home/debasish/PROGRAM/amber18/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) >> loadAmberParams frcmod.ionsjc_tip3p Loading parameters: /home/debasish/PROGRAM/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_126_tip3p Loading parameters: /home/debasish/PROGRAM/amber18/dat/leap/parm/frcmod.ions234lm_126_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 normal usage set) >> > > REC = loadpdb "1ua7.pdb" Loading PDB file: ./1ua7.pdb Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. Mapped residue ASP, term: Terminal/last, seq. number: 421 to: CASP. Created a new atom named: HN1 within residue: .R Created a new atom named: HN2 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R Created a new atom named: HN within residue: .R total atoms in file: 6403 Leap added 411 missing atoms according to residue templates: 411 H / lone pairs The file contained 422 atoms not in residue templates > solvateOct REC SPCBOX 14.0 Scaling up box by a factor of 1.234327 to meet diagonal cut criterion Solute vdw bounding box: 44.174 79.616 52.224 Total bounding box for atom centers: 114.177 114.177 114.177 (box expansion for 'iso' is 90.8%) Solvent unit box: 18.774 18.774 18.774 The number of boxes: x= 7 y= 7 z= 7 Volume: 763963.008 A^3 (oct) Mass > 425470.894 amu, Density > 0.925 g/cc (type - hence mass - of one or more atoms could not be found) Added 21022 residues. > addIons REC Cl- 3 Adding 3 counter ions to "REC" using 1A grid Used default radius 1.50 for 422 atoms Total solute charge: -14.00 Max atom radius: 1.98 Grid extends from solute vdw + 2.51 to 8.50 Box: enclosing: -35.80 -41.08 -39.53 37.63 31.62 42.86 sized: 92.20 86.92 88.47 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 3.43% of box, grid points 71856 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Cl- in REC at (23.31, -7.20, -31.76). (Replacing solvent molecule) Placed Cl- in REC at (16.67, 16.85, -15.72). (Replacing solvent molecule) Placed Cl- in REC at (-23.11, 14.17, -1.06). Done adding ions. > saveAmberParm REC solvated_1ua7.top solvated_1ua7.crd Checking Unit. Warning: The unperturbed charge of the unit (-17.000000) is not zero. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Error: Failed to generate parameters Warning: Parameter file was not saved.