logFile leap.log # # ----- leaprc for loading the Cornell et al. 1994 topologies # with parm99 # assumes that any unspecified nucleic acids are RNA # # load atom type hybridizations # addAtomTypes { { "H" "H" "sp3" } { "HO" "H" "sp3" } { "HS" "H" "sp3" } { "H1" "H" "sp3" } { "H2" "H" "sp3" } { "H3" "H" "sp3" } { "H4" "H" "sp3" } { "H5" "H" "sp3" } { "HW" "H" "sp3" } { "HC" "H" "sp3" } { "HA" "H" "sp3" } { "HP" "H" "sp3" } { "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. # parm99 = loadamberparams parm99.dat parm99 = loadamberparams trna.pcy # # Load DNA/RNA libraries # loadOff all_nucleic94.lib loadOff trna.lib # # Load main chain and terminating # amino acid libraries. # # tRNA only my changes Dec 10 # loadOff all_amino94.lib loadOff all_aminoct94.lib loadOff all_aminont94.lib # # Load ion library # loadOff ions94.lib # # # Load water library containing TIP3 UNIT and WATBOX216 periodic # box of 216 TIP3s. (These molecules are written to PDB as # "IP3" residues, so set IP3 = TIP3 for reading such PDBs.) # loadOff solvents.lib HOH = WAT IP3 = WAT # # Define the PDB name map for the amino acids and RNA. # 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" "RG5" } { 1 "GUA" "RG3" } { "GUA" "RG" } { 0 "ADE" "RA5" } { 1 "ADE" "RA3" } { "ADE" "RA" } { 0 "CYT" "RC5" } { 1 "CYT" "RC3" } { "CYT" "RC" } { 0 "URA" "RU5" } { 1 "URA" "RU3" } { "URA" "RU" } { 0 "G" "RG5" } { 1 "G" "RG3" } { "G" "RG" } { "GN" "RGN" } { 0 "A" "RA5" } { 1 "A" "RA3" } { "A" "RA" } { "AN" "RAN" } { 0 "C" "RC5" } { 1 "C" "RC3" } { "C" "RC" } { "CN" "RCN" } { 0 "U" "RU5" } { 1 "U" "RU3" } { "U" "RU" } { "UN" "RUN" } { 0 "C5" "RC5" } { 0 "G5" "RG5" } { 0 "A5" "RA5" } { 0 "U5" "RU5" } { 1 "C3" "RC3" } { 1 "G3" "RG3" } { 1 "A3" "RA3" } { 1 "U3" "RU3" } # #My entries # # #Modified bases # { "5GP" "5GP" } { "1MA" "1MA" } { "2MG" "2MG" } { "5MC" "5MC" } { "5MU" "5MU" } { "7MG" "7MG" } { "H2U" "H2U" } { "M2G" "M2G" } { "OMC" "OMC" } { "OMG" "OMG" } { "PSU" "PSU" } { "YG" "YG" } { "SPM" "SPM" } } addPdbAtomMap { { "O5*" "O5'" } { "C5*" "C5'" } { "C4*" "C4'" } { "O4*" "O4'" } { "C3*" "C3'" } { "O3*" "O3'" } { "O2*" "O2'" } { "C2*" "C2'" } { "C1*" "C1'" } # old ff atom names -> new { "O1'" "O4'" } { "OA" "O1P" } { "OB" "O2P" } { "H2'" "H2'1" } { "HO2'" "HO'2" } { "H5*1" "H5'1" } { "H5*2" "H5'2" } { "H4*" "H4'" } { "H3*" "H3'" } { "H1*" "H1'" } { "H2*1" "H2'1" } { "HO*2" "HO'2" } } # # assumed that most often users will want to use HID # NHIS = NHID HIS = HID CHIS = CHID # translate RNA residue names: GUA = RG CYT = RC ADE = RA URA = RU # my entries set default pdbwritecharges "on"