log started: Tue Oct 4 15:03:43 2011 Log file: ./ff94.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" } > { "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" } > { "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 1994 Cornell et al. force field. > # > # > # nucleic acids.. > # > loadAmberPrep all_nuc94.in Loading Prep file: /home/swails/build_amber/amber/dat/leap/prep/all_nuc94.in Warning: per-line charges being overridden by CHARGE block in D-ADENOSINE - with 5' - OH end group and 3' - O(minus) Warning: per-line charges being overridden by CHARGE block in D-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in D-ADENOSINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-ADENOSINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in R-ADENOSINE - with 5' - OH end group and 3' - O(minus) Warning: per-line charges being overridden by CHARGE block in R-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in R-ADENOSINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in R-ADENOSINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-THYMINE - with 5' - OH end group and 3' - O(minus) Warning: per-line charges being overridden by CHARGE block in D-THYMINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in D-THYMINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-THYMINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in R-URACIL - with 5' - OH end group and 3' - O(minus) Warning: per-line charges being overridden by CHARGE block in R-URACIL - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in R-URACIL - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in R-URACIL - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-GUANOSINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in R-GUANOSINE - with 5' - OH end group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in R-GUANOSINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in R-GUANOSINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in R-GUANOSINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-CYTOSINE - with 5' - OH end group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in D-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in D-CYTOSINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in D-CYTOSINE - with 5' - OH group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in R-CYTOSINE - with 5' - OH end group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in R-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group Warning: per-line charges being overridden by CHARGE block in R-CYTOSINE - with 5' - phosphate group and 3' - OH group Warning: per-line charges being overridden by CHARGE block in R-CYTOSINE - with 5' - OH group and 3' - OH group Loaded UNIT: DA Loaded UNIT: DA3 Loaded UNIT: DA5 Loaded UNIT: DAN Loaded UNIT: DC Loaded UNIT: DC3 Loaded UNIT: DC5 Loaded UNIT: DCN Loaded UNIT: DG Loaded UNIT: DG3 Loaded UNIT: DG5 Loaded UNIT: DGN Loaded UNIT: DT Loaded UNIT: DT3 Loaded UNIT: DT5 Loaded UNIT: DTN Loaded UNIT: RA Loaded UNIT: RA3 Loaded UNIT: RA5 Loaded UNIT: RAN Loaded UNIT: RC Loaded UNIT: RC3 Loaded UNIT: RC5 Loaded UNIT: RCN Loaded UNIT: RG Loaded UNIT: RG3 Loaded UNIT: RG5 Loaded UNIT: RGN Loaded UNIT: RU Loaded UNIT: RU3 Loaded UNIT: RU5 Loaded UNIT: RUN > # > a = { DA5 DT5 DG5 DC5 } > b = { DA3 DT3 DG3 DC3 } > c = { RA5 RU5 RG5 RC5 } > d = { RA3 RU3 RG3 RC3 } > e = { DA DT DG DC } > f = { RA RU RG RC } > g = { DAN DTN DGN DCN } > h = { RAN RUN RGN RCN } > # > set a restype nucleic > set DA5 head null > set DT5 head null > set DG5 head null > set DC5 head null > set b restype nucleic > set DA3 tail null > set DT3 tail null > set DG3 tail null > set DC3 tail null > set c restype nucleic > set RA5 head null > set RU5 head null > set RG5 head null > set RC5 head null > set d restype nucleic > set RA3 tail null > set RU3 tail null > set RG3 tail null > set RC3 tail null > set e restype nucleic > set f restype nucleic > set g restype nucleic > set DAN head null > set DAN tail null > set DTN head null > set DTN tail null > set DGN head null > set DGN tail null > set DCN head null > set DCN tail null > set h restype nucleic > set RAN head null > set RAN tail null > set RUN head null > set RUN tail null > set RGN head null > set RGN tail null > set RCN head null > set RCN tail null > # > saveOff a ./all_nucleic94.lib Saving DA5. Building topology. Building atom parameters. Saving DT5. Building topology. Building atom parameters. Saving DG5. Building topology. Building atom parameters. Saving DC5. Building topology. Building atom parameters. > saveOff b ./all_nucleic94.lib Saving DA3. Building topology. Building atom parameters. Saving DT3. Building topology. Building atom parameters. Saving DG3. Building topology. Building atom parameters. Saving DC3. Building topology. Building atom parameters. > saveOff c ./all_nucleic94.lib Saving RA5. Building topology. Building atom parameters. Saving RU5. Building topology. Building atom parameters. Saving RG5. Building topology. Building atom parameters. Saving RC5. Building topology. Building atom parameters. > saveOff d ./all_nucleic94.lib Saving RA3. Building topology. Building atom parameters. Saving RU3. Building topology. Building atom parameters. Saving RG3. Building topology. Building atom parameters. Saving RC3. Building topology. Building atom parameters. > saveOff e ./all_nucleic94.lib Saving DA. Building topology. Building atom parameters. Saving DT. Building topology. Building atom parameters. Saving DG. Building topology. Building atom parameters. Saving DC. Building topology. Building atom parameters. > saveOff f ./all_nucleic94.lib Saving RA. Building topology. Building atom parameters. Saving RU. Building topology. Building atom parameters. Saving RG. Building topology. Building atom parameters. Saving RC. Building topology. Building atom parameters. > saveOff g ./all_nucleic94.lib Saving DAN. Building topology. Building atom parameters. Saving DTN. Building topology. Building atom parameters. Saving DGN. Building topology. Building atom parameters. Saving DCN. Building topology. Building atom parameters. > saveOff h ./all_nucleic94.lib Saving RAN. Building topology. Building atom parameters. Saving RUN. Building topology. Building atom parameters. Saving RGN. Building topology. Building atom parameters. Saving RCN. Building topology. Building atom parameters. > # > # amino acids.. > # > ################################################ > ################################################ > ################################################ > ################################################ > ###### > ###### AMBER 94 prep.in files > ###### > ################################################ > ################################################ > ################################################ > ################################################ > #--------------------------------------------------- > # > # > # ALL ATOM FORCE FIELD > # > # > clearVariables Clearing all variables > # > # Extract the amino acids from all_amino94.in > # > loadAmberPrep all_amino94.in Loading Prep file: /home/swails/build_amber/amber/dat/leap/prep/all_amino94.in (no charges read on atoms lines in CYSTEINE with negative charge) ** CYSTEINE with negative charge: 'IMPROPER' atom HN not found (no charges read on atoms lines in NH2 ENDING GROUP) (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: 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_amino94.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.1 cend null > set NME head NME.1.N > set NME.1 connect0 NME.1.N > saveOff NME ./all_aminoct94.lib Saving NME. Building topology. Building atom parameters. > > set NHE restype protein > set NHE tail null > set NHE.1 cend null > set NHE head NHE.1.N > set NHE.1 connect0 NHE.1.N > saveOff NHE ./all_aminoct94.lib Saving NHE. Building topology. Building atom parameters. > > set ACE restype protein > set ACE head null > set ACE.1 nend null > set ACE tail ACE.1.C > set ACE.1 connect1 ACE.1.C > saveOff ACE ./all_aminont94.lib Saving ACE. Building topology. Building atom parameters. > > # > # Extract the N terminus residues > # > > clearVariables Clearing all variables > > loadAmberPrep all_aminont94.in N Loading Prep file: /home/swails/build_amber/amber/dat/leap/prep/all_aminont94.in Loaded UNIT: NALA Loaded UNIT: NARG Loaded UNIT: NASN Loaded UNIT: NASP Loaded UNIT: NCYS Loaded UNIT: NCYX 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 NCYX 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 NCYX.1 nend null > set NMET.1 nend null > > set a restype protein > set NCYX.1 disulphide NCYX.1.SG > saveOff a ./all_aminont94.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 NCYX. Building topology. Building atom parameters. Saving NMET. Building topology. Building atom parameters. > > # > # Extract the C terminus residues > # > > loadAmberPrep all_aminoct94.in C Loading Prep file: /home/swails/build_amber/amber/dat/leap/prep/all_aminoct94.in Loaded UNIT: CALA Loaded UNIT: CARG Loaded UNIT: CASN Loaded UNIT: CASP Loaded UNIT: CCYS Loaded UNIT: CCYX 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 CCYX 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 CCYX.1 cend null > set CMET.1 cend null > > set a restype protein > set CCYX.1 disulphide CCYX.1.SG > saveOff a ./all_aminoct94.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 CCYX. Building topology. Building atom parameters. Saving CMET. Building topology. Building atom parameters. > > # > # DONE ff94 > # > quit Quit