log started: Wed Feb 15 10:08:12 2012 Log file: ./ff03.log > addPath ../prep ../prep added to file search path. > addPath ../parm ../parm added to file search path. > addAtomTypes { > { "H" "H" "sp3" } > { "HO" "H" "sp3" } > { "HS" "H" "sp3" } > { "H0" "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" "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" } > { "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" } > { "EP" "" "sp3" } > # glycam > { "OG" "O" "sp3" } > { "OL" "O" "sp3" } > { "AC" "C" "sp3" } > { "EC" "C" "sp3" } > } > # > # leap .cmd script for building the residue > # libraries for the 2003 Duan et. all protein force field > # > # > # > # amino acids.. > # > ################################################ > ################################################ > ################################################ > ################################################ > ###### > ###### AMBER 03 prep.in files > ###### > ################################################ > ################################################ > ################################################ > ################################################ > #--------------------------------------------------- > # > # > # ALL ATOM FORCE FIELD > # > # > clearVariables Clearing all variables > # > # Extract the amino acids from all_amino03.in > # > loadAmberPrep all_amino03.in Loading Prep file: /home/case/amber11/dat/leap/prep/all_amino03.in Warning: per-line charges being overridden by CHARGE block in ALANINE Warning: per-line charges being overridden by CHARGE block in GLYCINE Warning: per-line charges being overridden by CHARGE block in SERINE Warning: per-line charges being overridden by CHARGE block in THREONINE Warning: per-line charges being overridden by CHARGE block in LEUCINE Warning: per-line charges being overridden by CHARGE block in ISOLEUCINE Warning: per-line charges being overridden by CHARGE block in VALINE Warning: per-line charges being overridden by CHARGE block in ASPARAGINE Warning: per-line charges being overridden by CHARGE block in GLUTAMINE Warning: per-line charges being overridden by CHARGE block in ARGININE Warning: per-line charges being overridden by CHARGE block in HISTIDINE DELTAH Warning: per-line charges being overridden by CHARGE block in HISTIDINE EPSILONH Warning: per-line charges being overridden by CHARGE block in HISTIDINE PLUS Warning: per-line charges being overridden by CHARGE block in TRYPTOPHAN Warning: per-line charges being overridden by CHARGE block in PHENYLALANINE Warning: per-line charges being overridden by CHARGE block in TYROSINE Warning: per-line charges being overridden by CHARGE block in GLUTAMIC ACID Warning: per-line charges being overridden by CHARGE block in ASPARTIC ACID Warning: per-line charges being overridden by CHARGE block in LYSINE Warning: per-line charges being overridden by CHARGE block in LYSINE neutral Warning: per-line charges being overridden by CHARGE block in PROLINE Warning: per-line charges being overridden by CHARGE block in CYSTEINE Warning: per-line charges being overridden by CHARGE block in CYSTEINE with negative charge Warning: per-line charges being overridden by CHARGE block in CYSTINE(S-S BRIDGE) Warning: per-line charges being overridden by CHARGE block in METHIONINE Warning: per-line charges being overridden by CHARGE block in ACE BEGINNING GROUP Warning: per-line charges being overridden by CHARGE block in N-methyl all atom (no charges read on atoms lines in NH2 ENDING GROUP) Warning: per-line charges being overridden by CHARGE block in ASP neutral Warning: per-line charges being overridden by CHARGE block in GLU neutral (UNKNOWN ATOM TYPE: IP) (UNKNOWN ATOM TYPE: IM) Loaded UNIT: ACE Loaded UNIT: ALA Loaded UNIT: ARG Loaded UNIT: ASH Loaded UNIT: ASN Loaded UNIT: ASP Loaded UNIT: CIM Loaded UNIT: CIP Loaded UNIT: CYM Loaded UNIT: CYS Loaded UNIT: CYX Loaded UNIT: GLH Loaded UNIT: GLN Loaded UNIT: GLU Loaded UNIT: GLY Loaded UNIT: HID Loaded UNIT: HIE Loaded UNIT: HIP Loaded UNIT: HOH Loaded UNIT: ILE Loaded UNIT: LEU Loaded UNIT: LYN Loaded UNIT: LYS Loaded UNIT: MET Loaded UNIT: NHE Loaded UNIT: NME Loaded UNIT: PHE Loaded UNIT: PRO Loaded UNIT: SER Loaded UNIT: THR Loaded UNIT: TRP Loaded UNIT: TYR Loaded UNIT: VAL > > a = { > ALA GLY SER THR LEU ILE VAL ASN GLN ARG > HID HIE HIP TRP PHE TYR GLU ASP LYS LYN > PRO CYS CYX MET ASH GLH CYM > } > > set a restype protein > set CYX.1 disulphide CYX.1.SG > saveOff a ./all_amino03.lib Saving ALA. Building topology. Building atom parameters. Saving GLY. Building topology. Building atom parameters. Saving SER. Building topology. Building atom parameters. Saving THR. Building topology. Building atom parameters. Saving LEU. Building topology. Building atom parameters. Saving ILE. Building topology. Building atom parameters. Saving VAL. Building topology. Building atom parameters. Saving ASN. Building topology. Building atom parameters. Saving GLN. Building topology. Building atom parameters. Saving ARG. Building topology. Building atom parameters. Saving HID. Building topology. Building atom parameters. Saving HIE. Building topology. Building atom parameters. Saving HIP. Building topology. Building atom parameters. Saving TRP. Building topology. Building atom parameters. Saving PHE. Building topology. Building atom parameters. Saving TYR. Building topology. Building atom parameters. Saving GLU. Building topology. Building atom parameters. Saving ASP. Building topology. Building atom parameters. Saving LYS. Building topology. Building atom parameters. Saving LYN. Building topology. Building atom parameters. Saving PRO. Building topology. Building atom parameters. Saving CYS. Building topology. Building atom parameters. Saving CYX. Building topology. Building atom parameters. Saving MET. Building topology. Building atom parameters. Saving ASH. Building topology. Building atom parameters. Saving GLH. Building topology. Building atom parameters. Saving CYM. Building topology. Building atom parameters. > > set NME restype protein > set NME tail null > set NME head NME.1.N > set NME.1 connect0 NME.1.N > saveOff NME ./all_aminoct03.lib Saving NME. Building topology. Building atom parameters. > > set NHE restype protein > set NHE tail null > set NHE head NHE.1.N > set NHE.1 connect0 NHE.1.N > saveOff NHE ./all_aminoct03.lib Saving NHE. Building topology. Building atom parameters. > > set ACE restype protein > set ACE head null > set ACE tail ACE.1.C > set ACE.1 connect1 ACE.1.C > saveOff ACE ./all_aminont03.lib Saving ACE. Building topology. Building atom parameters. > > # > # Extract the N terminus residues > # > > clearVariables Clearing all variables > > loadAmberPrep all_aminont03.in Loading Prep file: /home/case/amber11/dat/leap/prep/all_aminont03.in Loaded UNIT: NALA Loaded UNIT: NARG Loaded UNIT: NASN Loaded UNIT: NASP Loaded UNIT: NCYS Loaded UNIT: NGLN Loaded UNIT: NGLU Loaded UNIT: NGLY Loaded UNIT: NHID Loaded UNIT: NHIE Loaded UNIT: NHIP Loaded UNIT: NILE Loaded UNIT: NLEU Loaded UNIT: NLYS Loaded UNIT: NMET Loaded UNIT: NPHE Loaded UNIT: NPRO Loaded UNIT: NSER Loaded UNIT: NTHR Loaded UNIT: NTRP Loaded UNIT: NTYR Loaded UNIT: NVAL > > a = { > NALA NGLY NSER NTHR NLEU NILE NVAL NASN NGLN NARG > NHID NHIE NHIP NTRP NPHE NTYR NGLU NASP NLYS NPRO > NCYS NMET > } > > set a head null > set NALA.1 nend null > set NGLY.1 nend null > set NSER.1 nend null > set NTHR.1 nend null > set NLEU.1 nend null > set NILE.1 nend null > set NVAL.1 nend null > set NASN.1 nend null > set NGLN.1 nend null > set NARG.1 nend null > set NHID.1 nend null > set NHIE.1 nend null > set NHIP.1 nend null > set NTRP.1 nend null > set NPHE.1 nend null > set NTYR.1 nend null > set NGLU.1 nend null > set NASP.1 nend null > set NLYS.1 nend null > set NPRO.1 nend null > set NCYS.1 nend null > set NMET.1 nend null > > set a restype protein > saveOff a ./all_aminont03.lib Saving NALA. Building topology. Building atom parameters. Saving NGLY. Building topology. Building atom parameters. Saving NSER. Building topology. Building atom parameters. Saving NTHR. Building topology. Building atom parameters. Saving NLEU. Building topology. Building atom parameters. Saving NILE. Building topology. Building atom parameters. Saving NVAL. Building topology. Building atom parameters. Saving NASN. Building topology. Building atom parameters. Saving NGLN. Building topology. Building atom parameters. Saving NARG. Building topology. Building atom parameters. Saving NHID. Building topology. Building atom parameters. Saving NHIE. Building topology. Building atom parameters. Saving NHIP. Building topology. Building atom parameters. Saving NTRP. Building topology. Building atom parameters. Saving NPHE. Building topology. Building atom parameters. Saving NTYR. Building topology. Building atom parameters. Saving NGLU. Building topology. Building atom parameters. Saving NASP. Building topology. Building atom parameters. Saving NLYS. Building topology. Building atom parameters. Saving NPRO. Building topology. Building atom parameters. Saving NCYS. Building topology. Building atom parameters. Saving NMET. Building topology. Building atom parameters. > > # > # Extract the C terminus residues > # > > loadAmberPrep all_aminoct03.in Loading Prep file: /home/case/amber11/dat/leap/prep/all_aminoct03.in Loaded UNIT: CALA Loaded UNIT: CARG Loaded UNIT: CASN Loaded UNIT: CASP Loaded UNIT: CCYS Loaded UNIT: CGLN Loaded UNIT: CGLU Loaded UNIT: CGLY Loaded UNIT: CHID Loaded UNIT: CHIE Loaded UNIT: CHIP Loaded UNIT: CILE Loaded UNIT: CLEU Loaded UNIT: CLYS Loaded UNIT: CMET Loaded UNIT: CPHE Loaded UNIT: CPRO Loaded UNIT: CSER Loaded UNIT: CTHR Loaded UNIT: CTRP Loaded UNIT: CTYR Loaded UNIT: CVAL > > a = { > CALA CGLY CSER CTHR CLEU CILE CVAL CASN CGLN CARG > CHID CHIE CHIP CTRP CPHE CTYR CGLU CASP CLYS CPRO > CCYS CMET > } > > set a tail null > set CALA.1 cend null > set CGLY.1 cend null > set CSER.1 cend null > set CTHR.1 cend null > set CLEU.1 cend null > set CILE.1 cend null > set CVAL.1 cend null > set CASN.1 cend null > set CGLN.1 cend null > set CARG.1 cend null > set CHID.1 cend null > set CHIE.1 cend null > set CHIP.1 cend null > set CTRP.1 cend null > set CPHE.1 cend null > set CTYR.1 cend null > set CGLU.1 cend null > set CASP.1 cend null > set CLYS.1 cend null > set CPRO.1 cend null > set CCYS.1 cend null > set CMET.1 cend null > > set a restype protein > saveOff a ./all_aminoct03.lib Saving CALA. Building topology. Building atom parameters. Saving CGLY. Building topology. Building atom parameters. Saving CSER. Building topology. Building atom parameters. Saving CTHR. Building topology. Building atom parameters. Saving CLEU. Building topology. Building atom parameters. Saving CILE. Building topology. Building atom parameters. Saving CVAL. Building topology. Building atom parameters. Saving CASN. Building topology. Building atom parameters. Saving CGLN. Building topology. Building atom parameters. Saving CARG. Building topology. Building atom parameters. Saving CHID. Building topology. Building atom parameters. Saving CHIE. Building topology. Building atom parameters. Saving CHIP. Building topology. Building atom parameters. Saving CTRP. Building topology. Building atom parameters. Saving CPHE. Building topology. Building atom parameters. Saving CTYR. Building topology. Building atom parameters. Saving CGLU. Building topology. Building atom parameters. Saving CASP. Building topology. Building atom parameters. Saving CLYS. Building topology. Building atom parameters. Saving CPRO. Building topology. Building atom parameters. Saving CCYS. Building topology. Building atom parameters. Saving CMET. Building topology. Building atom parameters. > > # > # DONE ff03 > # > quit Quit