log started: Wed Jul 23 15:11:42 2003 Log file: ./leap.log >> # >> # ----- leaprc for loading the Cornell et al. 1994 force field. >> # assumes that any unspecified nucleic acids are DNA >> # >> # 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" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "C2" "C" "sp3" } >> { "C3" "C" "sp3" } >> { "C" "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" } >> { "CE" "C" "sp2" } >> { "CF" "C" "sp2" } >> { "CG" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp2" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "C" "sp2" } >> { "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" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "F" "F" "sp3" } >> { "CL" "Cl" "sp3" } >> { "BR" "Br" "sp3" } >> { "I" "I" "sp3" } >> { "FE" "Fe" "sp3" } >> # glycam >> { "OG" "O" "sp3" } >> { "OL" "O" "sp3" } >> { "AC" "C" "sp3" } >> { "EC" "C" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> parm94 = loadamberparams parm94.dat Loading parameters: /home/guille/amber7/dat/leap/parm/parm94.dat (UNKNOWN ATOM TYPE: IM) (UNKNOWN ATOM TYPE: Li) (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: K) (UNKNOWN ATOM TYPE: Rb) (UNKNOWN ATOM TYPE: Cs) (UNKNOWN ATOM TYPE: IB) (UNKNOWN ATOM TYPE: EP) >> # >> # Load DNA/RNA libraries >> # >> loadOff all_nucleic94.lib Loading library: /home/guille/amber7/dat/leap/lib/all_nucleic94.lib Loading: DA Loading: DA3 Loading: DA5 Loading: DAN Loading: DC Loading: DC3 Loading: DC5 Loading: DCN Loading: DG Loading: DG3 Loading: DG5 Loading: DGN Loading: DT Loading: DT3 Loading: DT5 Loading: DTN Loading: RA Loading: RA3 Loading: RA5 Loading: RAN Loading: RC Loading: RC3 Loading: RC5 Loading: RCN Loading: RG Loading: RG3 Loading: RG5 Loading: RGN Loading: RU Loading: RU3 Loading: RU5 Loading: RUN >> # >> # Load main chain and terminating >> # amino acid libraries. >> # >> loadOff all_amino94.lib Loading library: /home/guille/amber7/dat/leap/lib/all_amino94.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: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff all_aminoct94.lib Loading library: /home/guille/amber7/dat/leap/lib/all_aminoct94.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: 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 all_aminont94.lib Loading library: /home/guille/amber7/dat/leap/lib/all_aminont94.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> >> loadOff ions94.lib Loading library: /home/guille/amber7/dat/leap/lib/ions94.lib Loading: CIO Loading: Cl- Loading: Cs+ Loading: IB Loading: K+ Loading: Li+ Loading: Na+ Loading: Rb+ >> loadOff solvents.lib Loading library: /home/guille/amber7/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: MEOHBOX Loading: NMABOX Loading: PL3 Loading: POL3BOX Loading: SPC Loading: TIP4PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: WATBOX216 >> HOH = TP3 >> WAT = TP3 >> >> # >> # Define the PDB name map for the amino acids and DNA. >> # >> addPdbResMap { >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } >> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } >> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } >> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } >> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" } >> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" } >> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" } >> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" } >> { 0 "C5" "DC5" } >> { 0 "G5" "DG5" } >> { 0 "A5" "DA5" } >> { 0 "T5" "DT5" } >> { 1 "C3" "DC3" } >> { 1 "G3" "DG3" } >> { 1 "A3" "DA3" } >> { 1 "T3" "DT3" } >> >> } >> >> addPdbAtomMap { >> { "O5*" "O5'" } >> { "C5*" "C5'" } >> { "C4*" "C4'" } >> { "O4*" "O4'" } >> { "C3*" "C3'" } >> { "O3*" "O3'" } >> { "C2*" "C2'" } >> { "C1*" "C1'" } >> { "C5M" "C7" } >> { "H1*" "H1'" } >> { "H2*1" "H2'1" } >> { "H2*2" "H2'2" } >> { "H3*" "H3'" } >> { "H4*" "H4'" } >> { "H5*1" "H5'1" } >> { "H5*2" "H5'2" } >> # old ff atom names -> new >> { "O1'" "O4'" } >> { "OA" "O1P" } >> { "OB" "O2P" } >> } >> >> # >> # assumed that most often users will want to use HID >> # >> NHIS = NHID >> HIS = HID >> CHIS = CHID >> > > source modelurea.in ----- Source: ./modelurea.in ----- Source of ./modelurea.in done >> uu = loadpdb sg3m.pdb Loading PDB file: ./sg3m.pdb Matching PDB residue names to LEaP variables. (Residue 0: MIE, Terminal/last, was not found in name map.) Unknown residue: MIE number: 0 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 1: MD1, Terminal/last, was not found in name map.) Unknown residue: MD1 number: 1 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 2: CRB, Terminal/last, was not found in name map.) Unknown residue: CRB number: 2 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 3: MD2, Terminal/last, was not found in name map.) Unknown residue: MD2 number: 3 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 4: MD3, Terminal/last, was not found in name map.) Unknown residue: MD3 number: 4 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 5: ACT, Terminal/last, was not found in name map.) Unknown residue: ACT number: 5 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 6: NIO, Terminal/last, was not found in name map.) Unknown residue: NIO number: 6 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck (Residue 7: URE, Terminal/last, was not found in name map.) Unknown residue: URE number: 7 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Creating new UNIT for residue: MIE sequence: 1 Created a new atom named: ND1 within residue: .R Created a new atom named: CG within residue: .R Created a new atom named: CE1 within residue: .R Created a new atom named: CB within residue: .R Created a new atom named: CD2 within residue: .R Created a new atom named: NE2 within residue: .R Created a new atom named: HE1 within residue: .R Created a new atom named: HB1 within residue: .R Created a new atom named: HB2 within residue: .R Created a new atom named: HB3 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HE2 within residue: .R Creating new UNIT for residue: MD1 sequence: 2 Created a new atom named: NE2 within residue: .R Created a new atom named: CD2 within residue: .R Created a new atom named: CE1 within residue: .R Created a new atom named: CG within residue: .R Created a new atom named: ND1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HE1 within residue: .R Created a new atom named: CB within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HB1 within residue: .R Created a new atom named: HB2 within residue: .R Created a new atom named: HB3 within residue: .R Creating new UNIT for residue: CRB sequence: 3 Created a new atom named: OD1 within residue: .R Created a new atom named: CG within residue: .R Created a new atom named: ND within residue: .R Created a new atom named: OD2 within residue: .R Created a new atom named: CA within residue: .R Created a new atom named: H within residue: .R Created a new atom named: HB1 within residue: .R Created a new atom named: HB2 within residue: .R Created a new atom named: HB3 within residue: .R Creating new UNIT for residue: MD2 sequence: 4 Created a new atom named: NE2 within residue: .R Created a new atom named: CD2 within residue: .R Created a new atom named: CE1 within residue: .R Created a new atom named: CG within residue: .R Created a new atom named: ND1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HE1 within residue: .R Created a new atom named: CB within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HB1 within residue: .R Created a new atom named: HB2 within residue: .R Created a new atom named: HB3 within residue: .R Creating new UNIT for residue: MD3 sequence: 5 Created a new atom named: NE2 within residue: .R Created a new atom named: CD2 within residue: .R Created a new atom named: CE1 within residue: .R Created a new atom named: CG within residue: .R Created a new atom named: ND1 within residue: .R Created a new atom named: HD2 within residue: .R Created a new atom named: HE1 within residue: .R Created a new atom named: CB within residue: .R Created a new atom named: HD1 within residue: .R Created a new atom named: HB1 within residue: .R Created a new atom named: HB2 within residue: .R Created a new atom named: HB3 within residue: .R Creating new UNIT for residue: ACT sequence: 6 Created a new atom named: OD1 within residue: .R Created a new atom named: CG within residue: .R Created a new atom named: CB within residue: .R Created a new atom named: OD2 within residue: .R Created a new atom named: HB1 within residue: .R Created a new atom named: HB2 within residue: .R Created a new atom named: HB3 within residue: .R Creating new UNIT for residue: NIO sequence: 7 Created a new atom named: NI1 within residue: .R Created a new atom named: NI2 within residue: .R Created a new atom named: HNI within residue: .R Created a new atom named: ONI within residue: .R Creating new UNIT for residue: URE sequence: 8 Created a new atom named: NU1 within residue: .R Created a new atom named: HU2 within residue: .R Created a new atom named: CU1 within residue: .R Created a new atom named: HU1 within residue: .R Created a new atom named: OU1 within residue: .R Created a new atom named: NU2 within residue: .R Created a new atom named: HU4 within residue: .R Created a new atom named: HU3 within residue: .R total atoms in file: 76 The file contained 76 atoms not in residue templates >> source ni29u.src ----- Source: ./ni29u.src ----- Source of ./ni29u.src done >>> nu= loadamberparams ni1u29l_urease.param Loading parameters: ./ni1u29l_urease.param Reading force field mod type file (frcmod) Unknown keyword: in parameter file. (UNKNOWN ATOM TYPE: NU) (UNKNOWN ATOM TYPE: ON) >>> ny= loadamberparams ni2y29l_urease.param Loading parameters: ./ni2y29l_urease.param Reading force field mod type file (frcmod) (UNKNOWN ATOM TYPE: NY) >>> set uu.7.1 name NI1 >>> set uu.7.2 name NI2 >>> set uu.7.3 name ONI >>> set uu.7.4 name HNI >>> set uu.7.1 type NU >>> set uu.7.2 type NY >>> set uu.7.3 type ON >>> set uu.7.4 type HO >>> >>> set uu.7.1 charge 0.915341 >>> set uu.7.2 charge 0.752448 >>> set uu.7.3 charge -0.436524 >>> set uu.7.4 charge 0.441331 >>> >>> bond uu.7.1 uu.7.3 >>> bond uu.7.2 uu.7.3 Bond: Maximum coordination exceeded on .R.A -- setting atoms pert=true overrides default limits >>> bond uu.7.3 uu.7.4 Bond: maximum coordination exceeded on .R.A -- setting atoms pert=true overrides default limits >>> bond uu.7.1 uu.1.1 >>> bond uu.7.1 uu.2.1 >>> bond uu.7.1 uu.3.1 >>> bond uu.7.2 uu.3.4 >>> bond uu.7.2 uu.4.1 >>> bond uu.7.2 uu.5.1 >>> bond uu.7.2 uu.6.1 >>> bond uu.7.1 uu.8.5 >>> bond uu.7.2 uu.8.6 >>> >> >> source actu.src ----- Source: ./actu.src ----- Source of ./actu.src done >>> bondbydistance uu.6 Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance 9 pairs of atoms within potential bonding distance 6 are not H-H pairs Created 6 bonds. >>> set uu.6.1 type O2 >>> set uu.6.2 type C >>> set uu.6.3 type CT >>> set uu.6.4 type O2 >>> set uu.6.5 type HC >>> set uu.6.6 type HC >>> set uu.6.7 type HC >>> >>> set uu.6.1 charge -0.680635 >>> set uu.6.2 charge 0.852491 >>> set uu.6.3 charge -0.449439 >>> set uu.6.4 charge -0.685949 >>> set uu.6.5 charge 0.116053 >>> set uu.6.6 charge 0.116053 >>> set uu.6.7 charge 0.116053 >>> >>> >>> >>> >>> >>> >>> >> >> source crb29u.src ----- Source: ./crb29u.src ----- Source of ./crb29u.src done >>> bondbydistance uu.3 Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance 11 pairs of atoms within potential bonding distance 8 are not H-H pairs Created 8 bonds. >>> ou= loadamberparams ogu_urease.param Loading parameters: ./ogu_urease.param Reading force field mod type file (frcmod) Unknown keyword: in parameter file. (UNKNOWN ATOM TYPE: OU) >>> oy= loadamberparams ogy_urease.param Loading parameters: ./ogy_urease.param Reading force field mod type file (frcmod) (UNKNOWN ATOM TYPE: OY) >>> cg= loadamberparams c7u_urease.param Loading parameters: ./c7u_urease.param Reading force field mod type file (frcmod) Unknown keyword: in parameter file. (UNKNOWN ATOM TYPE: C7) >>> ng= loadamberparams ngu_urease.param Loading parameters: ./ngu_urease.param Reading force field mod type file (frcmod) Unknown keyword: in parameter file. (UNKNOWN ATOM TYPE: NG) >>> set uu.3.1 type OU >>> set uu.3.2 type C7 >>> set uu.3.3 type NG >>> set uu.3.4 type OY >>> set uu.3.5 type CT >>> set uu.3.6 type H >>> set uu.3.7 type HC >>> set uu.3.8 type HC >>> set uu.3.9 type HC >>> >>> set uu.3.1 charge -0.678465 >>> set uu.3.2 charge 0.77512 >>> set uu.3.3 charge -0.516482 >>> set uu.3.4 charge -0.71577 >>> set uu.3.5 charge 0.143644 >>> set uu.3.6 charge 0.308861 >>> set uu.3.7 charge 0.016905 >>> set uu.3.8 charge 0.016905 >>> set uu.3.9 charge 0.016905 >>> >>> >>> >>> >>> >>> >> >> source mie29u.src ----- Source: ./mie29u.src ----- Source of ./mie29u.src done >>> bondbydistance uu.1 Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance 15 pairs of atoms within potential bonding distance 12 are not H-H pairs Created 12 bonds. >>> nm= loadamberparams nmu_urease.param Loading parameters: ./nmu_urease.param Reading force field mod type file (frcmod) Unknown keyword: in parameter file. (UNKNOWN ATOM TYPE: NM) >>> set uu.1.1 name ND1 >>> set uu.1.2 name CG >>> set uu.1.3 name CE1 >>> set uu.1.4 name CB >>> set uu.1.5 name CD2 >>> set uu.1.6 name NE2 >>> set uu.1.7 name HE1 >>> set uu.1.8 name HB1 >>> set uu.1.9 name HB2 >>> set uu.1.10 name HB3 >>> set uu.1.11 name HD2 >>> set uu.1.12 name HE2 >>> set uu.1.1 type NM >>> set uu.1.2 type CC >>> set uu.1.3 type CR >>> set uu.1.4 type CT >>> set uu.1.5 type CW >>> set uu.1.6 type NA >>> set uu.1.7 type H5 >>> set uu.1.8 type HC >>> set uu.1.9 type HC >>> set uu.1.10 type HC >>> set uu.1.11 type H4 >>> set uu.1.12 type H >>> >>> set uu.1.1 charge -0.366683 >>> set uu.1.2 charge 0.446199 >>> set uu.1.3 charge 0.032611 >>> set uu.1.4 charge -0.663926 >>> set uu.1.5 charge -0.335790 >>> set uu.1.6 charge -0.155472 >>> set uu.1.7 charge 0.119097 >>> set uu.1.8 charge 0.19139 >>> set uu.1.9 charge 0.19139 >>> set uu.1.10 charge 0.19139 >>> set uu.1.11 charge 0.211640 >>> set uu.1.12 charge 0.324732 >> >> source mid129u.src ----- Source: ./mid129u.src ----- Source of ./mid129u.src done >>> bondbydistance uu.2 Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance 15 pairs of atoms within potential bonding distance 12 are not H-H pairs Created 12 bonds. >>> nt= loadamberparams n4u_urease.param Loading parameters: ./n4u_urease.param Reading force field mod type file (frcmod) Unknown keyword: in parameter file. (UNKNOWN ATOM TYPE: N4) >>> set uu.2.1 type N4 >>> set uu.2.2 type CV >>> set uu.2.3 type CR >>> set uu.2.4 type CC >>> set uu.2.5 type NA >>> set uu.2.6 type H4 >>> set uu.2.7 type H5 >>> set uu.2.8 type CT >>> set uu.2.9 type H >>> set uu.2.10 type HC >>> set uu.2.11 type HC >>> set uu.2.12 type HC >>> >>> set uu.2.1 charge -0.49369 >>> set uu.2.2 charge 0.065955 >>> set uu.2.3 charge 0.123996 >>> set uu.2.4 charge 0.181009 >>> set uu.2.5 charge -0.283237 >>> set uu.2.6 charge 0.045639 >>> set uu.2.7 charge 0.095628 >>> set uu.2.8 charge -0.528973 >>> set uu.2.9 charge 0.335115 >>> set uu.2.10 charge 0.171352 >>> set uu.2.11 charge 0.171352 >>> set uu.2.12 charge 0.171352 >>> >>> >>> >>> >> >> source mid229u.src ----- Source: ./mid229u.src ----- Source of ./mid229u.src done >>> bondbydistance uu.4 Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance 15 pairs of atoms within potential bonding distance 12 are not H-H pairs Created 12 bonds. >>> np= loadamberparams niy_urease.param Loading parameters: ./niy_urease.param Reading force field mod type file (frcmod) Unknown keyword: in parameter file. (UNKNOWN ATOM TYPE: NI) >>> set uu.4.1 type NI >>> set uu.4.2 type CV >>> set uu.4.3 type CR >>> set uu.4.4 type CC >>> set uu.4.5 type NA >>> set uu.4.6 type H4 >>> set uu.4.7 type H5 >>> set uu.4.8 type CT >>> set uu.4.9 type H >>> set uu.4.10 type HC >>> set uu.4.11 type HC >>> set uu.4.12 type HC >>> >>> set uu.4.1 charge -0.466296 >>> set uu.4.2 charge -0.186163 >>> set uu.4.3 charge 0.461017 >>> set uu.4.4 charge 0.379811 >>> set uu.4.5 charge -0.542830 >>> set uu.4.6 charge 0.122833 >>> set uu.4.7 charge 0.035923 >>> set uu.4.8 charge -0.591765 >>> set uu.4.9 charge 0.369538 >>> set uu.4.10 charge 0.178397 >>> set uu.4.11 charge 0.178397 >>> set uu.4.12 charge 0.178397 >>> >>> >>> >>> >>> >> >> source mid329u.src ----- Source: ./mid329u.src ----- Source of ./mid329u.src done >>> bondbydistance uu.5 Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance 15 pairs of atoms within potential bonding distance 12 are not H-H pairs Created 12 bonds. >>> ne= loadamberparams ney_urease.param Loading parameters: ./ney_urease.param Reading force field mod type file (frcmod) Unknown keyword: in parameter file. (UNKNOWN ATOM TYPE: NE) >>> set uu.5.1 type NE >>> set uu.5.2 type CV >>> set uu.5.3 type CR >>> set uu.5.4 type CC >>> set uu.5.5 type NA >>> set uu.5.6 type H4 >>> set uu.5.7 type H5 >>> set uu.5.8 type CT >>> set uu.5.9 type H >>> set uu.5.10 type HC >>> set uu.5.11 type HC >>> set uu.5.12 type HC >>> >>> set uu.5.1 charge -0.207334 >>> set uu.5.2 charge -0.097916 >>> set uu.5.3 charge 0.015586 >>> set uu.5.4 charge 0.190368 >>> set uu.5.5 charge -0.282492 >>> set uu.5.6 charge 0.137228 >>> set uu.5.7 charge 0.146629 >>> set uu.5.8 charge -0.466307 >>> set uu.5.9 charge 0.336009 >>> set uu.5.10 charge 0.151309 >>> set uu.5.11 charge 0.151309 >>> set uu.5.12 charge 0.151309 >>> >>> >>> >>> >>> >> >> source urea.src ----- Source: ./urea.src ----- Source of ./urea.src done >>> bondbydistance uu.8 Hydrogens .R.A and .R.A within bonding distance Hydrogens .R.A and .R.A within bonding distance 10 pairs of atoms within potential bonding distance 8 are not H-H pairs Atom .R.A has maximum number of bonds. Created 7 bonds. >>> o1= loadamberparams o1urea.param Loading parameters: ./o1urea.param Reading force field mod type file (frcmod) (UNKNOWN ATOM TYPE: O1) >>> c1= loadamberparams c1urea.param Loading parameters: ./c1urea.param Reading force field mod type file (frcmod) (UNKNOWN ATOM TYPE: C1) >>> n1= loadamberparams n1urea.param Loading parameters: ./n1urea.param Reading force field mod type file (frcmod) (UNKNOWN ATOM TYPE: N1) >>> n2= loadamberparams n2urea.param Loading parameters: ./n2urea.param Reading force field mod type file (frcmod) >>> set uu.8.1 type N1 >>> set uu.8.2 type H >>> set uu.8.3 type C1 >>> set uu.8.4 type H >>> set uu.8.5 type O1 >>> set uu.8.6 type N2 >>> set uu.8.7 type H >>> set uu.8.8 type H >>> >>> set uu.8.1 charge -0.3078 >>> set uu.8.2 charge 0.1220 >>> set uu.8.3 charge 0.7165 >>> set uu.8.4 charge 0.1220 >>> set uu.8.5 charge -0.6844 >>> set uu.8.6 charge -0.5072 >>> set uu.8.7 charge 0.4169 >>> set uu.8.8 charge 0.1220 >>> >>> >>> >>> >>> >>> >> >> check uu Checking 'uu'.... WARNING: The unperturbed charge of the unit: 1.009879 is not zero. Warning: Close contact of 0.966699 angstroms between .R.A and .R.A Checking parameters for unit 'uu'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. >> saveamberparm uu sg3m22.top sg3m22.crd Checking Unit. WARNING: The unperturbed charge of the unit: 1.009879 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 21 improper torsions applied Building H-Bond parameters. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected ACT 1 CRB 1 MD1 1 MD2 1 MD3 1 MIE 1 NIO 1 URE 1 ) (no restraints)