1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 28a1 August 15, 1999 Copyright(c) 1984,1992 President and Fellows of Harvard College All Rights Reserved Current operating system: IRIS UNIX Created on 5/24/ 0 at 11:56:29 by user: crowley Maximum number of ATOMS: 60120, and RESidues: 32000 Current HEAP size: 10240000, and STACK size: 900000 Processing passed argument "pdbfile=1fsc" Parameter: PDBFILE <- "1FSC" Processing passed argument "solvate=true" Parameter: SOLVATE <- "TRUE" Processing passed argument "crystal=true" Parameter: CRYSTAL <- "TRUE" Processing passed argument "shape=octahedral" Parameter: SHAPE <- "OCTAHEDRAL" RDTITL> * THIS IS A GENERAL TEMPLATE SCRIPT TO CREATE A SOLVATED RDTITL> * SIMULATION "box" USING PERIODIC BOUNDARIES WITH A FEW SPECIFIC VOLUMES. RDTITL> * THE SCRIPT WILL GENERATE, MINIMIZE (OR ALTERNATIVELY READ IN A PSF RDTITL> * FILE FOR A SOLUTE SYSTEM ALREADY GENERATED) A SOLUTE SYSTEM IN A: RDTITL> * 1) CUBIC VOLUME W/ IMAGES OR CRYSTAL RDTITL> * 2) TRUNCATED OCTAHEDRAL BOX W/ IMAGES RDTITL> * 3) TRUNCATED OCTAHEDRAL BOX W/ CRYSTAL (REORIENTED FROM IMAGES) RDTITL> *** RDTITL> * REQUIRED FILES: TOP_ALL22_PROT.INP, PAR_ALL22_PROT.INP RDTITL> ** OCTA.IMG, TIP125.CRD, TIP216.CRD RDTITL> * CHARMM> CHARMM> CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !* IMPORTANT USAGE NOTE: ONLY SINGLE CHAIN PROTEINS CAN BE PROCESSED CHARMM> !* WITH GENERATION/MINIMAZATION STAGE BECAUSE OF PSF GENERATION PROCEDURE CHARMM> !* USED, I.E. ASSUMPTION THAT PSF CAN BE GENERATED BY READING SEQUENCE OF CHARMM> !* PROTEIN FROM PDB FILE. CHARMM> !* FOR MORE GENERAL SOLVATION PROBLEMS, I.E. MULTI-CHAIN PROTEINS, CHARMM> !* SIMPLY JUST USE THE PSF=TRUE KEY AND THE SOLVATION PART. CHARMM> !**_______________________________________________________________________** CHARMM> !** WRITTEN BY C.L. BROOKS, III ** CHARMM> !** OCTOBER, 1999 ** CHARMM> !** ** CHARMM> !** COPYRIGHT C.L. BROOKS, III, THE SCRIPPS RESEARCH INSTITUTE ** CHARMM> !**_______________________________________________________________________** CHARMM> !******** CHARMM> !* The usage requires that several variables either be set in the CHARMM> !* input script or on the CHARMM command line at execution. CHARMM> !* The needed variables are: CHARMM> !** Variable Default Function CHARMM> !*__________________________________________________________________________ CHARMM> !* toppar ($toppar) ==> path to parameter and topology files CHARMM> !** CHARMM> !* pdbfile (...) ==> name of pdb coordinate file containing CHARMM> !** coordinates and sequence information CHARMM> !** (for psf=true key this is the name of the CHARMM> !** coordinate file in pdb format (pdbfile.pdb) CHARMM> !** and the pre-generated psf file (pdbfile.psf)) CHARMM> !* psf (false) ==> key specifying use of pre-generated psf and CHARMM> !** pdb coordinate file for use w/ multi-segid CHARMM> !** solute systems CHARMM> !* seqname (pdbfile) ==> name of protein sequence (segid) CHARMM> !** CHARMM> !* shape (cubic) ==> variable specifying whether truncated octahedral or CHARMM> !** cubic volume used (octahedral/cubic) CHARMM> !* crystal (false) ==> logical variable true/false specifying whether CHARMM> !** to use crystal orientation of simulation volume CHARMM> !* cutoff (9) ==> value of cutoff to be used in establishing how CHARMM> !** far images are to be from volume "edges", often set CHARMM> !** at or near nonbonded list cutoff value CHARMM> !** to use crystal orientation of simulation volume CHARMM> !* solvate (false) ==> logical flag which determines whether you stop after CHARMM> !** initial minimization and psf generation or proceed CHARMM> !** to solvation component. CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> CHARMM> if @?pdbfile eq 0 goto iamdead Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> if @?seqname eq 0 set seqname = @pdbfile Parameter: PDBFILE -> "1FSC" Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: SEQNAME <- "1FSC" CHARMM> if @?psf eq 0 set psf = false Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: PSF <- "FALSE" CHARMM> if @?toppar eq 0 set toppar = "$toppar" Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: TOPPAR <- ""$toppar"" CHARMM> if @?shape eq 0 set shape = cubic Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> if @?crystal eq 0 set crystal = false Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> if @?cutoff eq 0 set cutoff = 9 Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: CUTOFF <- "9" CHARMM> if @?solvate eq 0 set solvate = false Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> !prnlev 0 node 0 CHARMM> !wrnlev 0 node 0 CHARMM> open unit 1 read form name "@TOPPAR/top_all22_prot.inp" Parameter: TOPPAR -> ""$toppar"" VOPEN> Attempting to open::/cb/monet3/charmm/MFC/c27b1/toppar/top_all22_prot.inp:: OPNLGU> Unit 1 opened for READONLY access to /cb/monet3/charmm/MFC/c27b1/toppar/top_all22_prot.inp CHARMM> read rtf card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>> AUGUST 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<< TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU <<<<<<<<< TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 read form name "@TOPPAR/par_all22_prot.inp" Parameter: TOPPAR -> ""$toppar"" VOPEN> Attempting to open::/cb/monet3/charmm/MFC/c27b1/toppar/par_all22_prot.inp:: OPNLGU> Unit 1 opened for READONLY access to /cb/monet3/charmm/MFC/c27b1/toppar/par_all22_prot.inp CHARMM> read param card unit 1 PARAMETER FILE BEING READ FROM UNIT 1 TITLE> *>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>> AUGUST 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<< TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU <<<<<<<<< TITLE> * PARRDR> Multiple terms for dihedral type: INDEX 443 CODE36924784 CT3 -OS -CD -OB PARRDR> Multiple terms for dihedral type: INDEX 441 CODE36919834 CT2 -OS -CD -OB PARRDR> Multiple terms for dihedral type: INDEX 434 CODE36611445 CP3 -N -C -O PARRDR> Multiple terms for dihedral type: INDEX 432 CODE36605676 CP2 -CP1 -C -O PARRDR> Multiple terms for dihedral type: INDEX 430 CODE36601545 CP1 -N -C -O PARRDR> Multiple terms for dihedral type: INDEX 421 CODE36486876 HB -CP1 -C -O PARRDR> Multiple terms for dihedral type: INDEX 406 CODE31833876 N -CP1 -C -NH1 PARRDR> Multiple terms for dihedral type: INDEX 404 CODE31734876 CP2 -CP1 -C -NH1 PARRDR> Multiple terms for dihedral type: INDEX 398 CODE31616076 HB -CP1 -C -NH1 PARRDR> Multiple terms for dihedral type: INDEX 387 CODE30715176 CP2 -CP1 -C -N PARRDR> Multiple terms for dihedral type: INDEX 381 CODE30596376 HB -CP1 -C -N PARRDR> Multiple terms for dihedral type: INDEX 353 CODE26632451 CT3 -NH1 -C -CP1 PARRDR> Multiple terms for dihedral type: INDEX 351 CODE26627501 CT2 -NH1 -C -CP1 PARRDR> Multiple terms for dihedral type: INDEX 349 CODE26622551 CT1 -NH1 -C -CP1 PARRDR> Multiple terms for dihedral type: INDEX 334 CODE25984001 CT2 -NH1 -C -CT3 PARRDR> Multiple terms for dihedral type: INDEX 332 CODE25979051 CT1 -NH1 -C -CT3 PARRDR> Multiple terms for dihedral type: INDEX 326 CODE25921463 HS -S -CT2 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 325 CODE25921463 HS -S -CT2 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 323 CODE25876301 H -OH1 -CT2 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 322 CODE25876301 H -OH1 -CT2 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 320 CODE25876300 H -OH1 -CT1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 319 CODE25876300 H -OH1 -CT1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 311 CODE25865201 CT1 -NH1 -C -CT2 PARRDR> Multiple terms for dihedral type: INDEX 306 CODE25762451 H -OH1 -CT2 -CT2 PARRDR> Multiple terms for dihedral type: INDEX 305 CODE25762451 H -OH1 -CT2 -CT2 PARRDR> Multiple terms for dihedral type: INDEX 295 CODE25698713 HS -S -CT2 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 294 CODE25698713 HS -S -CT2 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 292 CODE25653551 H -OH1 -CT2 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 291 CODE25653551 H -OH1 -CT2 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 289 CODE25653550 H -OH1 -CT1 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 288 CODE25653550 H -OH1 -CT1 -CT1 PARRDR> Multiple terms for dihedral type: INDEX 242 CODE12103275 CP2 -CP1 -CC -O PARRDR> Multiple terms for dihedral type: INDEX 240 CODE11984475 HB -CP1 -CC -O PARRDR> Multiple terms for dihedral type: INDEX 226 CODE 7598775 N -CP1 -CC -NH2 PARRDR> Multiple terms for dihedral type: INDEX 224 CODE 7499775 CP2 -CP1 -CC -NH2 PARRDR> Multiple terms for dihedral type: INDEX 222 CODE 7380975 HB -CP1 -CC -NH2 PARRDR> Multiple terms for dihedral type: INDEX 189 CODE 6311676 N -C -CP1 -N PARRDR> Multiple terms for dihedral type: INDEX 181 CODE 2446545 CP1 -C -N -CP3 PARRDR> Multiple terms for dihedral type: INDEX 179 CODE 2421795 CT3 -C -N -CP3 PARRDR> Multiple terms for dihedral type: INDEX 177 CODE 2416845 CT2 -C -N -CP3 PARRDR> Multiple terms for dihedral type: INDEX 175 CODE 2411895 CT1 -C -N -CP3 PARRDR> Multiple terms for dihedral type: INDEX 169 CODE 2154495 CP1 -C -N -CP1 PARRDR> Multiple terms for dihedral type: INDEX 167 CODE 2129745 CT3 -C -N -CP1 PARRDR> Multiple terms for dihedral type: INDEX 165 CODE 2124795 CT2 -C -N -CP1 PARRDR> Multiple terms for dihedral type: INDEX 163 CODE 2119845 CT1 -C -N -CP1 PARRDR> Multiple terms for dihedral type: INDEX 132 CODE 1604123 CT3 -CT2 -CPH1-CPH1 PARRDR> Multiple terms for dihedral type: INDEX 131 CODE 1604123 CT3 -CT2 -CPH1-CPH1 PARRDR> Multiple terms for dihedral type: INDEX 128 CODE 1594223 CT1 -CT2 -CPH1-CPH1 PARRDR> Multiple terms for dihedral type: INDEX 127 CODE 1594223 CT1 -CT2 -CPH1-CPH1 PARRDR> Multiple terms for dihedral type: INDEX 120 CODE 1488403 CT3 -SM -SM -CT3 PARRDR> Multiple terms for dihedral type: INDEX 119 CODE 1488403 CT3 -SM -SM -CT3 PARRDR> Multiple terms for dihedral type: INDEX 117 CODE 1488263 CT3 -CT2 -S -CT3 PARRDR> Multiple terms for dihedral type: INDEX 115 CODE 1486451 CT3 -C -NH1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 112 CODE 1483313 CT2 -CT2 -S -CT3 PARRDR> Multiple terms for dihedral type: INDEX 110 CODE 1481501 CT2 -C -NH1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 107 CODE 1476551 CT1 -C -NH1 -CT3 PARRDR> Multiple terms for dihedral type: INDEX 99 CODE 1369603 CT2 -SM -SM -CT2 PARRDR> Multiple terms for dihedral type: INDEX 98 CODE 1369603 CT2 -SM -SM -CT2 PARRDR> Multiple terms for dihedral type: INDEX 96 CODE 1367651 CT2 -C -NH1 -CT2 PARRDR> Multiple terms for dihedral type: INDEX 93 CODE 1362701 CT1 -C -NH1 -CT2 PARRDR> Multiple terms for dihedral type: INDEX 83 CODE 1253801 CT1 -C -NH1 -CT1 PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> prnlev 5 node 0 **** Warning **** The following extraneous characters were found while command processing in MISCOM NODE 0 CHARMM> wrnlev 2 node 0 **** Warning **** The following extraneous characters were found while command processing in MISCOM NODE 0 CHARMM> CHARMM> if psf ne true goto buildprotein Comparing "FALSE" and "TRUE". IF test evaluated as true. Performing command CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> ! SOLUTE GENERATION COMPONENT: ASSUMES SINGLE CHAIN SOLUTE IN PDB ! CHARMM> ! FILE GIVEN BY KEY PDBFILE. IF MORE THAN ONE CHAIN IS PRESENT ! CHARMM> ! THE GENERATION ASPECTS WILL BE ERRONEOUS. ! CHARMM> ! THIS COMPONENT OF THE SCRIPT: ! CHARMM> ! 1) GENERATES PROTEIN SEQUENCE ! CHARMM> ! 2) BUILDS ALL MISSING ATOMS ! CHARMM> ! 3) MINIMIZES PROTEIN SUBJECT TO SUCCESSIVELY REDUCED HARMONIC RESTRAINTS ! CHARMM> ! 4) WRITES THE MINIMIZED PDB FILE ! CHARMM> ! CHECKS ARE DONE ON NUMBER OF MISSING ATOMS TO GUESS WHETHER FILE WAS ! CHARMM> ! PROCESSED CORRECTLY. EXAMINE OUTPUT FILE FOR POTENTIAL PROBLEMS! ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> ! Copy original file for safe keeping then "fix" pdb file CHARMM> system "echo @PDBFILE.pdb > filename" Parameter: PDBFILE -> "1FSC" Invoking: echo 1FSC.pdb > filename CHARMM> system "cp `awk '{print tolower($0)}' filename` pdb_orig" Invoking: cp `awk '{print tolower($0)}' filename` pdb_orig CHARMM> CHARMM> ! Make "standard" changes to accomodate pdb -> top_all22/28 atom/residue renames. CHARMM> system "echo 'BEGIN {write = 1}' > awk.file" Invoking: echo 'BEGIN {write = 1}' > awk.file CHARMM> system "echo '$1 == "ENDMDL" {write = 0;}'>> awk.file" Invoking: echo '$1 == "ENDMDL" {write = 0;}'>> awk.file CHARMM> system "echo '$1 == "END" {print $0}'>> awk.file" Invoking: echo '$1 == "END" {print $0}'>> awk.file CHARMM> system "echo '{if ( write == 1 ) {' >> awk.file" Invoking: echo '{if ( write == 1 ) {' >> awk.file CHARMM> system "echo 'if ($4 == "HIS" && $5 == "6") sub("HIS","HSD");' >> awk.file" Invoking: echo 'if ($4 == "HIS" && $5 == "6") sub("HIS","HSD");' >> awk.file CHARMM> system "echo 'if ($4 == "HIS" && $5 == "29") sub("HIS","HSE");' >> awk.file" Invoking: echo 'if ($4 == "HIS" && $5 == "29") sub("HIS","HSE");' >> awk.file CHARMM> system "echo 'if ($1 == "ATOM") {print $0}' >> awk.file" Invoking: echo 'if ($1 == "ATOM") {print $0}' >> awk.file CHARMM> system "echo '}}'>> awk.file" Invoking: echo '}}'>> awk.file CHARMM> system "awk -f awk.file pdb_orig > pdb_new" Invoking: awk -f awk.file pdb_orig > pdb_new CHARMM> CHARMM> ! Clean-up temporary files CHARMM> system "rm awk.file" Invoking: rm awk.file CHARMM> system "mv pdb_new `(awk '{print tolower($0)}' filename)`" Invoking: mv pdb_new `(awk '{print tolower($0)}' filename)` CHARMM> CHARMM> open unit 1 read form name @PDBFILE.pdb Parameter: PDBFILE -> "1FSC" VOPEN> Attempting to open::1fsc.pdb:: OPNLGU> Unit 1 opened for READONLY access to 1fsc.pdb CHARMM> read sequ pdb unit 1 MAINIO> Sequence information being read from unit 1. TITLE> * RESIDUE SEQUENCE -- 61 RESIDUES THR MET CYS TYR SER HSD THR THR THR SER ARG ALA ILE LEU THR ASN CYS GLY GLU ASN SER CYS TYR ARG LYS SER ARG ARG HSE PRO PRO LYS MET VAL LEU GLY ARG GLY CYS GLY CYS PRO PRO GLY ASP ASP ASN LEU GLU VAL LYS CYS CYS THR SER PRO ASP LYS CYS ASN TYR ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 12 TITRATABLE GROUPS THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF HIS - 0 ASP - 3 GLU - 2 LYS - 4 TYR - 3 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> prnlev 6 CHARMM> generate @seqname setup first nter last cter Parameter: SEQNAME -> "1FSC" THE PATCH 'NTER ' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CTER ' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is 1FSC. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 61 Number of atoms = 914 Number of groups = 259 Number of bonds = 923 Number of angles = 1658 Number of dihedrals = 2436 Number of impropers = 159 Number of HB acceptors = 92 Number of HB donors = 127 Number of NB exclusions = 0 Total charge = 4.00000 CHARMM> CHARMM> ! Check for disulphide bonds in SSBOND records CHARMM> system "echo "* Disuplhides for @pdbfile" > disu.strm" Parameter: PDBFILE -> "1FSC" Invoking: echo "* DISUPLHIDES FOR 1FSC" > disu.strm CHARMM> system "echo "* " >> disu.strm" Invoking: echo "* " >> disu.strm CHARMM> system "awk '$1 == "SSBOND" {print "patch disu @pdbfile",$4," @pdbfile",$6}' pdb_orig >> disu.strm" Parameter: PDBFILE -> "1FSC" Parameter: PDBFILE -> "1FSC" Invoking: awk '$1 == "SSBOND" {print "PATCH DISU 1FSC",$4," 1FSC",$6}' pdb_orig >> disu.strm CHARMM> CHARMM> stream "disu.strm" VOPEN> Attempting to open::disu.strm:: OPNLGU> Unit 99 opened for READONLY access to disu.strm INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * DISUPLHIDES FOR 1FSC RDTITL> * Parameter: IN1 <- "" CHARMM> PATCH DISU 1FSC 3 1FSC 22 ATOM 1FSC 3 CYS HG1 AND ALL REFERENCES TO IT DELETED. ATOM 1FSC 22 CYS HG1 AND ALL REFERENCES TO IT DELETED. Message from MAPIC: Atom numbers are changed. DELTIC: 2 bonds deleted DELTIC: 2 angles deleted DELTIC: 6 dihedrals deleted DELTIC: 2 donors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 61 Number of atoms = 912 Number of groups = 259 Number of bonds = 922 Number of angles = 1658 Number of dihedrals = 2437 Number of impropers = 159 Number of HB acceptors = 92 Number of HB donors = 125 Number of NB exclusions = 0 Total charge = 4.00000 CHARMM> PATCH DISU 1FSC 17 1FSC 39 ATOM 1FSC 17 CYS HG1 AND ALL REFERENCES TO IT DELETED. ATOM 1FSC 39 CYS HG1 AND ALL REFERENCES TO IT DELETED. Message from MAPIC: Atom numbers are changed. DELTIC: 2 bonds deleted DELTIC: 2 angles deleted DELTIC: 6 dihedrals deleted DELTIC: 2 donors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 61 Number of atoms = 910 Number of groups = 259 Number of bonds = 921 Number of angles = 1658 Number of dihedrals = 2438 Number of impropers = 159 Number of HB acceptors = 92 Number of HB donors = 123 Number of NB exclusions = 0 Total charge = 4.00000 CHARMM> PATCH DISU 1FSC 41 1FSC 52 ATOM 1FSC 41 CYS HG1 AND ALL REFERENCES TO IT DELETED. ATOM 1FSC 52 CYS HG1 AND ALL REFERENCES TO IT DELETED. Message from MAPIC: Atom numbers are changed. DELTIC: 2 bonds deleted DELTIC: 2 angles deleted DELTIC: 6 dihedrals deleted DELTIC: 2 donors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 61 Number of atoms = 908 Number of groups = 259 Number of bonds = 920 Number of angles = 1658 Number of dihedrals = 2439 Number of impropers = 159 Number of HB acceptors = 92 Number of HB donors = 121 Number of NB exclusions = 0 Total charge = 4.00000 CHARMM> PATCH DISU 1FSC 53 1FSC 59 ATOM 1FSC 53 CYS HG1 AND ALL REFERENCES TO IT DELETED. ATOM 1FSC 59 CYS HG1 AND ALL REFERENCES TO IT DELETED. Message from MAPIC: Atom numbers are changed. DELTIC: 2 bonds deleted DELTIC: 2 angles deleted DELTIC: 6 dihedrals deleted DELTIC: 2 donors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 61 Number of atoms = 906 Number of groups = 259 Number of bonds = 919 Number of angles = 1658 Number of dihedrals = 2440 Number of impropers = 159 Number of HB acceptors = 92 Number of HB donors = 119 Number of NB exclusions = 0 Total charge = 4.00000 VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> system "rm disu.strm" Invoking: rm disu.strm CHARMM> CHARMM> rename atom cd1 select resname ile .and. type cd end SELRPN> 1 atoms have been selected out of 906 FOR SEGMENT '1FSC' RESIDUE '13 ', ATOM 'CD ' IS RENAMED TO 'CD1 ' CHARMM> rename atom oxt select type ot1 end SELRPN> 1 atoms have been selected out of 906 FOR SEGMENT '1FSC' RESIDUE '61 ', ATOM 'OT1 ' IS RENAMED TO 'OXT ' CHARMM> rename atom o select ires ?nres .and. type ot2 end RDCMND substituted energy or value "?NRES" to "61" SELRPN> 1 atoms have been selected out of 906 FOR SEGMENT '1FSC' RESIDUE '61 ', ATOM 'OT2 ' IS RENAMED TO 'O ' CHARMM> open unit 1 read form name @PDBFILE.pdb Parameter: PDBFILE -> "1FSC" VOPEN> Attempting to open::1fsc.pdb:: OPNLGU> Unit 1 opened for READONLY access to 1fsc.pdb CHARMM> read coor pdb unit 1 SPATIAL COORDINATES BEING READ FROM UNIT 1 TITLE> * ** WARNING ** After reading, there are no coordinates for selected atom: 2 1 THR HT1 ** WARNING ** After reading, there are no coordinates for selected atom: 3 1 THR HT2 ** WARNING ** After reading, there are no coordinates for selected atom: 4 1 THR HT3 ** WARNING ** After reading, there are no coordinates for selected atom: 6 1 THR HA ** WARNING ** After reading, there are no coordinates for selected atom: 8 1 THR HB ** WARNING ** After reading, there are no coordinates for selected atom: 10 1 THR HG1 ** WARNING ** After reading, there are no coordinates for selected atom: 12 1 THR HG21 ** WARNING ** After reading, there are no coordinates for selected atom: 13 1 THR HG22 ** WARNING ** After reading, there are no coordinates for selected atom: 14 1 THR HG23 ** WARNING ** After reading, there are no coordinates for selected atom: 18 2 MET HN ** A total of 442 selected atoms have no coordinates *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> rename atom cd select resname ile .and. type cd1 end SELRPN> 1 atoms have been selected out of 906 FOR SEGMENT '1FSC' RESIDUE '13 ', ATOM 'CD1 ' IS RENAMED TO 'CD ' CHARMM> rename atom ot1 select type oxt end SELRPN> 1 atoms have been selected out of 906 FOR SEGMENT '1FSC' RESIDUE '61 ', ATOM 'OXT ' IS RENAMED TO 'OT1 ' CHARMM> rename atom ot2 select ires ?nres .and. type o end RDCMND substituted energy or value "?NRES" to "61" SELRPN> 1 atoms have been selected out of 906 FOR SEGMENT '1FSC' RESIDUE '61 ', ATOM 'O ' IS RENAMED TO 'OT2 ' CHARMM> CHARMM> ! Now move original pdb file back and fnish clean-up CHARMM> system "mv pdb_orig `awk '{print tolower($0)}' filename`" Invoking: mv pdb_orig `awk '{print tolower($0)}' filename` CHARMM> system "rm filename" Invoking: rm filename CHARMM> CHARMM> define nonH select .not. hydrogen end SELRPN> 464 atoms have been selected out of 906 CHARMM> set nonHatoms = ?nsel RDCMND substituted energy or value "?NSEL" to "464" Parameter: NONHATOMS <- "464" CHARMM> define missing select .not. hydrogen .and. .not. initialized end SELRPN> 0 atoms have been selected out of 906 CHARMM> set missingatoms = ?nsel RDCMND substituted energy or value "?NSEL" to "0" Parameter: MISSINGATOMS <- "0" CHARMM> CHARMM> Calc fraction = (@nonHatoms - @missingatoms) / @nonHatoms Parameter: NONHATOMS -> "464" Parameter: MISSINGATOMS -> "0" Parameter: NONHATOMS -> "464" Evaluating: (464-0)/464 Parameter: FRACTION <- "1" CHARMM> if fraction le 0.8 goto toomanywrong Comparing "1" and "0.8". IF test evaluated as false. Skipping command CHARMM> CHARMM> print coor select missing end SELRPN> 0 atoms have been selected out of 906 ***** LEVEL 2 WARNING FROM ***** ***** ZERO ATOMS SPECIFIED TO WRITE. NO FILE CREATED ****************************************** BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 2 CHARMM> CHARMM> ! Build missing atoms if just a few CHARMM> ic param CHARMM> ic build ALL POSSIBLE COORDINATES HAVE BEEN PLACED CHARMM> CHARMM> hbuild CHARMM> CHARMM> define missing select .not. initialized end SELRPN> 0 atoms have been selected out of 906 CHARMM> if nsel ne 0 goto skipthis Comparing "NSEL" and "0". IF test evaluated as true. Performing command CHARMM> CHARMM> open unit 1 write form name @pdbfile.psf Parameter: PDBFILE -> "1FSC" VOPEN> Attempting to open::1fsc.psf:: OPNLGU> Unit 1 opened for WRITE access to 1fsc.psf CHARMM> write psf card unit 1 RDTITL> RDTITL> No title read. CHARMM> CHARMM> open unit 1 write form name @pdbfile_NOTmin.pdb Parameter: PDBFILE -> "1FSC" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::1fsc_notmin.pdb:: OPNLGU> Unit 1 opened for WRITE access to 1fsc_notmin.pdb CHARMM> write coor pdb unit 1 RDTITL> RDTITL> No title read. CHARMM> CHARMM> coor copy compare SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> coor orie ORIENT THE COORDINATES TO ALIGN WITH AXIS MOMENTS 53452.64549647 12869.34079912 -15485.82336922 33057.11797992 -16661.12450909 36065.52277156 Transpose of the rotation matrix 0.516113 -0.454608 -0.725920 -0.505299 0.522721 -0.686611 0.691593 0.721175 0.040070 CENTER OF ATOMS BEFORE TRANSLATION 3.67686 19.35811 0.93684 AXIS OF ROTATION IS -0.704442 0.709308 0.025365 ANGLE IS 87.74 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coor stat STATISTICS FOR 906 SELECTED ATOMS: XMIN = -17.639572 XMAX = 17.961035 XAVE = 0.000000 YMIN = -20.059022 YMAX = 11.591666 YAVE = 0.000000 ZMIN = -11.132372 ZMAX = 10.542244 ZAVE = 0.000000 WMIN = 0.000000 WMAX = 69.460000 WAVE = 14.251755 CHARMM> faster on MISCOM> FAST option ON. Scalar FAST Mode CHARMM> CHARMM> set k 30.0 Parameter: K <- "30.0" CHARMM> label minimize CHARMM> CHARMM> cons harm force @k select .not. hydrogen end Parameter: K -> "30.0" SELRPN> 464 atoms have been selected out of 906 CSTRAN: Harmonic Restraints ABSOlute type as set number 1. Number of selected atoms: 464 Reference coordinates set to main coordinates. Mass weighting will NOT be used for new restraints. The force constant of 30.00000 will be used. An exponent of 2 will be used. The XYZ scale factors are: 1.00000 1.00000 1.00000 A total of 464 atoms are restrained. CHARMM> CHARMM> minimize conj nstep 500 tolenr 0.001 - CHARMM> cutnb 14.0 rdie eps 2.0 vswitch shift NONBOND OPTION FLAGS: ELEC VDW ATOMs RDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 2.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 2577 exclusions and 2396 interactions(1-4) found 746 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 260340 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 189597 ATOM PAIRS WERE FOUND FOR ATOM LIST 7036 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 500 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0010000 TOLGRD = 0.0000000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- MINI> 0 1957.57315 0.00000 104.63274 0.00000 MINI INTERN> 91.08434 666.71636 286.36025 304.92203 7.99540 MINI EXTERN> 910.90837 -310.41360 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 172.96710 1784.60605 3.59372 0.31235 MINI INTERN> 36.38651 231.12417 58.85400 294.91503 3.86481 MINI EXTERN> -191.37478 -306.63569 0.00000 0.00000 0.00000 MINI CONSTR> 45.83304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 58.72348 114.24362 2.54361 0.28063 MINI INTERN> 26.29124 164.14551 27.43668 288.79830 3.97273 MINI EXTERN> -217.05015 -309.81335 0.00000 0.00000 0.00000 MINI CONSTR> 74.94252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 14.02924 44.69423 2.01325 0.26909 MINI INTERN> 24.39728 123.75741 13.21221 292.18303 4.27081 MINI EXTERN> -213.67172 -311.79624 0.00000 0.00000 0.00000 MINI CONSTR> 81.67647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -9.54354 23.57279 1.40122 0.16463 MINI INTERN> 22.67682 112.54502 10.01409 290.91705 3.92232 MINI EXTERN> -214.50937 -313.57956 0.00000 0.00000 0.00000 MINI CONSTR> 78.47009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -22.34351 12.79997 1.13082 0.13923 MINI INTERN> 22.08953 112.16759 8.76925 287.07264 3.98372 MINI EXTERN> -216.76188 -314.82457 0.00000 0.00000 0.00000 MINI CONSTR> 75.16022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -29.18408 6.84057 0.93486 0.11076 MINI INTERN> 21.58855 114.31494 9.72912 285.05147 3.61610 MINI EXTERN> -216.81290 -315.09510 0.00000 0.00000 0.00000 MINI CONSTR> 68.42374 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -33.78335 4.59927 0.65251 0.07515 MINI INTERN> 21.66214 112.23875 8.75387 283.18265 3.74381 MINI EXTERN> -217.69796 -314.89382 0.00000 0.00000 0.00000 MINI CONSTR> 69.22721 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -37.33639 3.55303 0.75377 0.10592 MINI INTERN> 21.73281 111.02748 8.30461 280.94649 3.64347 MINI EXTERN> -218.12999 -314.77393 0.00000 0.00000 0.00000 MINI CONSTR> 69.91268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -40.59945 3.26307 0.69668 0.09700 MINI INTERN> 21.66821 112.81485 9.21768 278.52010 3.82265 MINI EXTERN> -218.48744 -314.48674 0.00000 0.00000 0.00000 MINI CONSTR> 66.33125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -43.33348 2.73403 0.54508 0.08208 MINI INTERN> 21.04835 110.78198 8.92233 277.66553 3.89100 MINI EXTERN> -216.80938 -314.38993 0.00000 0.00000 0.00000 MINI CONSTR> 65.55663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 260340 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 189362 ATOM PAIRS WERE FOUND FOR ATOM LIST 7039 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -43.33348 2.73403 0.54508 0.00000 MINI INTERN> 21.04835 110.78198 8.92233 277.66553 3.89100 MINI EXTERN> -216.80938 -314.38993 0.00000 0.00000 0.00000 MINI CONSTR> 65.55663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 110 -46.31975 2.98626 0.28736 0.03897 MINI INTERN> 21.31950 109.07261 8.46560 277.38839 3.81830 MINI EXTERN> -218.47437 -314.58542 0.00000 0.00000 0.00000 MINI CONSTR> 66.67565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 120 -47.30805 0.98830 0.18487 0.04112 MINI INTERN> 21.11685 108.27932 8.24906 276.96569 3.70846 MINI EXTERN> -218.36060 -314.69275 0.00000 0.00000 0.00000 MINI CONSTR> 67.42592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 130 -47.61468 0.30663 0.10961 0.02021 MINI INTERN> 21.11881 108.16703 8.27066 276.75025 3.73044 MINI EXTERN> -218.68468 -314.79322 0.00000 0.00000 0.00000 MINI CONSTR> 67.82604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 140 -47.72039 0.10571 0.05132 0.01019 MINI INTERN> 21.15676 108.15409 8.27218 276.76374 3.74282 MINI EXTERN> -218.78350 -314.79783 0.00000 0.00000 0.00000 MINI CONSTR> 67.77135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with function tolerance ( 0.0010000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 149 -47.74197 0.02157 0.02261 0.02000 CONJ INTERN> 21.13669 108.25039 8.28972 276.81815 3.73433 CONJ EXTERN> -218.74215 -314.76333 0.00000 0.00000 0.00000 CONJ CONSTR> 67.53423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> coor orie rms select type ca end SELRPN> 61 atoms have been selected out of 906 CENTER OF ATOMS BEFORE TRANSLATION -0.70528 0.58649 0.46115 CENTER OF REFERENCE COORDINATE SET 3.33505 20.31623 1.06582 NET TRANSLATION OF ROTATED ATOMS 4.04033 19.72974 0.60467 ROTATION MATRIX 0.516248 -0.454465 -0.725913 -0.505521 0.522492 -0.686623 0.691330 0.721432 0.039994 AXIS OF ROTATION IS -0.704573 0.709171 0.025548 ANGLE IS 87.74 TOTAL SQUARE DIFF IS 0.0699 DENOMINATOR IS 61.0000 THUS RMS DIFF IS 0.033849 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coor orie rms select .not. hydrogen end SELRPN> 464 atoms have been selected out of 906 CENTER OF ATOMS BEFORE TRANSLATION 3.53668 19.61214 0.87733 CENTER OF REFERENCE COORDINATE SET 3.53680 19.61372 0.87606 NET TRANSLATION OF ROTATED ATOMS 0.00012 0.00158 -0.00127 ROTATION MATRIX 1.000000 -0.000367 0.000043 0.000367 1.000000 0.000066 -0.000043 -0.000066 1.000000 AXIS OF ROTATION IS 0.175578 -0.114992 -0.977727 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 2.2511 DENOMINATOR IS 464.0000 THUS RMS DIFF IS 0.069653 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> CHARMM> decr k by 10.0 Parameter: K <- "20" CHARMM> if k ge 10.0 goto minimize Comparing "20" and "10.0". IF test evaluated as true. Performing command CHARMM> CHARMM> cons harm force @k select .not. hydrogen end Parameter: K -> "20" SELRPN> 464 atoms have been selected out of 906 CSTRAN: Harmonic Restraints ABSOlute type as set number 1. Number of selected atoms: 464 Reference coordinates set to main coordinates. Mass weighting will NOT be used for new restraints. The force constant of 20.00000 will be used. An exponent of 2 will be used. The XYZ scale factors are: 1.00000 1.00000 1.00000 A total of 464 atoms are restrained. CHARMM> CHARMM> minimize conj nstep 500 tolenr 0.001 - CHARMM> cutnb 14.0 rdie eps 2.0 vswitch shift NONBOND OPTION FLAGS: ELEC VDW ATOMs RDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 2.000 NBXMOD = 5 There are 189362 atom pairs and 4973 atom exclusions. There are 0 group pairs and 746 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 260340 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 189354 ATOM PAIRS WERE FOUND FOR ATOM LIST 7192 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 500 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0010000 TOLGRD = 0.0000000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- MINI> 0 -115.27619 67.53423 1.72608 0.00000 MINI INTERN> 21.13669 108.25039 8.28972 276.81815 3.73433 MINI EXTERN> -218.74215 -314.76333 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -137.78585 22.50966 0.56256 0.07532 MINI INTERN> 21.97139 100.74476 6.75895 275.32610 3.25364 MINI EXTERN> -241.74532 -313.28574 0.00000 0.00000 0.00000 MINI CONSTR> 9.19036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -141.09106 3.30521 0.30702 0.04609 MINI INTERN> 21.55802 98.50551 6.62709 273.00895 3.35016 MINI EXTERN> -241.78324 -314.49779 0.00000 0.00000 0.00000 MINI CONSTR> 12.14025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -141.96054 0.86948 0.16631 0.02770 MINI INTERN> 21.38937 98.61991 6.60977 271.96635 3.33910 MINI EXTERN> -242.55160 -314.37930 0.00000 0.00000 0.00000 MINI CONSTR> 13.04585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -142.23112 0.27058 0.09335 0.01976 MINI INTERN> 21.44723 98.39515 6.61844 271.34030 3.33123 MINI EXTERN> -242.08818 -314.49982 0.00000 0.00000 0.00000 MINI CONSTR> 13.22453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -142.34305 0.11192 0.06511 0.01466 MINI INTERN> 21.47192 98.51077 6.61192 270.94006 3.32019 MINI EXTERN> -242.25215 -314.33640 0.00000 0.00000 0.00000 MINI CONSTR> 13.39065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -142.38882 0.04578 0.04124 0.00880 MINI INTERN> 21.46207 98.56118 6.62855 270.75432 3.31199 MINI EXTERN> -242.31080 -314.32612 0.00000 0.00000 0.00000 MINI CONSTR> 13.52998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -142.40833 0.01951 0.02620 0.00567 MINI INTERN> 21.44547 98.59057 6.61796 270.66640 3.31712 MINI EXTERN> -242.28991 -314.30411 0.00000 0.00000 0.00000 MINI CONSTR> 13.54816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with function tolerance ( 0.0010000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 73 -142.41143 0.00310 0.02390 0.02000 CONJ INTERN> 21.43948 98.58110 6.61904 270.66351 3.31993 CONJ EXTERN> -242.27487 -314.30704 0.00000 0.00000 0.00000 CONJ CONSTR> 13.54742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> coor orie rms select type ca end SELRPN> 61 atoms have been selected out of 906 CENTER OF ATOMS BEFORE TRANSLATION 3.33649 20.31865 1.06336 CENTER OF REFERENCE COORDINATE SET 3.33505 20.31623 1.06582 NET TRANSLATION OF ROTATED ATOMS -0.00144 -0.00242 0.00246 ROTATION MATRIX 1.000000 0.000561 -0.000169 -0.000561 1.000000 -0.000135 0.000169 0.000135 1.000000 AXIS OF ROTATION IS -0.223836 0.280342 0.933438 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 0.1814 DENOMINATOR IS 61.0000 THUS RMS DIFF IS 0.054532 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coor orie rms select .not. hydrogen end SELRPN> 464 atoms have been selected out of 906 CENTER OF ATOMS BEFORE TRANSLATION 3.53573 19.61137 0.87858 CENTER OF REFERENCE COORDINATE SET 3.53680 19.61372 0.87606 NET TRANSLATION OF ROTATED ATOMS 0.00107 0.00235 -0.00251 ROTATION MATRIX 1.000000 -0.000565 0.000166 0.000565 1.000000 0.000135 -0.000166 -0.000135 1.000000 AXIS OF ROTATION IS 0.223048 -0.275193 -0.935157 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 4.7190 DENOMINATOR IS 464.0000 THUS RMS DIFF IS 0.100848 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> CHARMM> decr k by 10.0 Parameter: K <- "10" CHARMM> if k ge 10.0 goto minimize Comparing "10" and "10.0". IF test evaluated as true. Performing command CHARMM> CHARMM> cons harm force @k select .not. hydrogen end Parameter: K -> "10" SELRPN> 464 atoms have been selected out of 906 CSTRAN: Harmonic Restraints ABSOlute type as set number 1. Number of selected atoms: 464 Reference coordinates set to main coordinates. Mass weighting will NOT be used for new restraints. The force constant of 10.00000 will be used. An exponent of 2 will be used. The XYZ scale factors are: 1.00000 1.00000 1.00000 A total of 464 atoms are restrained. CHARMM> CHARMM> minimize conj nstep 500 tolenr 0.001 - CHARMM> cutnb 14.0 rdie eps 2.0 vswitch shift NONBOND OPTION FLAGS: ELEC VDW ATOMs RDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 2.000 NBXMOD = 5 There are 189354 atom pairs and 4973 atom exclusions. There are 0 group pairs and 746 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 260340 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 189152 ATOM PAIRS WERE FOUND FOR ATOM LIST 7191 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 500 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0010000 TOLGRD = 0.0000000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- MINI> 0 -155.95885 13.54742 0.63255 0.00000 MINI INTERN> 21.43948 98.58110 6.61904 270.66351 3.31993 MINI EXTERN> -242.27487 -314.30704 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -166.20023 10.24138 0.50581 0.07315 MINI INTERN> 23.27612 98.24737 6.49552 269.33921 2.94793 MINI EXTERN> -256.80641 -314.83552 0.00000 0.00000 0.00000 MINI CONSTR> 5.13554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -168.97687 2.77664 0.28270 0.05073 MINI INTERN> 22.73516 96.86872 6.41019 266.60973 3.06074 MINI EXTERN> -256.77946 -316.04035 0.00000 0.00000 0.00000 MINI CONSTR> 8.15841 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -169.95362 0.97675 0.18649 0.03992 MINI INTERN> 22.55751 97.08140 6.40999 265.28223 3.04263 MINI EXTERN> -257.42673 -316.06712 0.00000 0.00000 0.00000 MINI CONSTR> 9.16647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -170.29423 0.34062 0.10290 0.02130 MINI INTERN> 22.56039 96.86600 6.37152 264.71318 3.01607 MINI EXTERN> -257.20107 -316.10437 0.00000 0.00000 0.00000 MINI CONSTR> 9.48404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -170.42252 0.12828 0.06993 0.01462 MINI INTERN> 22.56376 96.84472 6.37955 264.41097 3.01694 MINI EXTERN> -257.23322 -315.96312 0.00000 0.00000 0.00000 MINI CONSTR> 9.55788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -170.47681 0.05429 0.04342 0.00985 MINI INTERN> 22.59805 96.84341 6.38562 264.30266 3.00407 MINI EXTERN> -257.24355 -315.95103 0.00000 0.00000 0.00000 MINI CONSTR> 9.58397 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -170.50581 0.02900 0.03809 0.00994 MINI INTERN> 22.59205 96.89209 6.37460 264.25635 3.01218 MINI EXTERN> -257.27837 -315.93525 0.00000 0.00000 0.00000 MINI CONSTR> 9.58055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -170.52478 0.01897 0.02927 0.00829 MINI INTERN> 22.57891 96.87104 6.37393 264.23994 3.01017 MINI EXTERN> -257.25406 -315.93227 0.00000 0.00000 0.00000 MINI CONSTR> 9.58758 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with function tolerance ( 0.0010000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 88 -170.53444 0.00966 0.02438 0.02000 CONJ INTERN> 22.56786 96.87667 6.37053 264.21694 3.00850 CONJ EXTERN> -257.24761 -315.92162 0.00000 0.00000 0.00000 CONJ CONSTR> 9.59429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> coor orie rms select type ca end SELRPN> 61 atoms have been selected out of 906 CENTER OF ATOMS BEFORE TRANSLATION 3.33857 20.31980 1.06204 CENTER OF REFERENCE COORDINATE SET 3.33505 20.31623 1.06582 NET TRANSLATION OF ROTATED ATOMS -0.00352 -0.00357 0.00378 ROTATION MATRIX 1.000000 0.000798 -0.000341 -0.000798 1.000000 -0.000246 0.000341 0.000247 1.000000 AXIS OF ROTATION IS -0.273297 0.377981 0.884556 ANGLE IS 0.05 TOTAL SQUARE DIFF IS 0.3848 DENOMINATOR IS 61.0000 THUS RMS DIFF IS 0.079423 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coor orie rms select .not. hydrogen end SELRPN> 464 atoms have been selected out of 906 CENTER OF ATOMS BEFORE TRANSLATION 3.53382 19.61019 0.87992 CENTER OF REFERENCE COORDINATE SET 3.53680 19.61372 0.87606 NET TRANSLATION OF ROTATED ATOMS 0.00298 0.00353 -0.00385 ROTATION MATRIX 1.000000 -0.000799 0.000330 0.000798 1.000000 0.000241 -0.000330 -0.000240 1.000000 AXIS OF ROTATION IS 0.268155 -0.367683 -0.890451 ANGLE IS 0.05 TOTAL SQUARE DIFF IS 8.4517 DENOMINATOR IS 464.0000 THUS RMS DIFF IS 0.134963 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> CHARMM> decr k by 10.0 Parameter: K <- "0" CHARMM> if k ge 10.0 goto minimize Comparing "0" and "10.0". IF test evaluated as false. Skipping command CHARMM> CHARMM> open unit 1 write form name @pdbfile.psf Parameter: PDBFILE -> "1FSC" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::1fsc.psf:: OPNLGU> Unit 1 opened for WRITE access to 1fsc.psf CHARMM> write psf card unit 1 RDTITL> RDTITL> No title read. CHARMM> CHARMM> open unit 1 write form name @pdbfile_minimized.pdb Parameter: PDBFILE -> "1FSC" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::1fsc_minimized.pdb:: OPNLGU> Unit 1 opened for WRITE access to 1fsc_minimized.pdb CHARMM> write coor pdb unit 1 RDTITL> RDTITL> No title read. CHARMM> CHARMM> if solvate eq true goto solvate Comparing "TRUE" and "TRUE". IF test evaluated as true. Performing command CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> ! PROTEIN SOLVATION COMPONENT: SOLVATES PROTEIN SYSTEM IN SOLVENT VOLUME ! CHARMM> ! GIVEN BY KEYS SHAPE AND CRYSTAL AND CUTOFF ! CHARMM> ! THIS COMPONENT OF THE SCRIPT: ! CHARMM> ! 1) DETERMINES THE OPTIMAL SIZE FOR SOLVATION VOLUME ! CHARMM> ! 2) CONSTRUCTS A CUBIC VOLUME OF APPROPRIATE SIZE FROM BUILDING BLOCKS ! CHARMM> ! 3) CONSTRUCTS REQUESTED VOLUME FROM THIS CUBE AND WRITES FILE ! CHARMM> ! 4) DELETES OVERLAPPING WATER MOLECULES ! CHARMM> ! 5) WRITES CHARMM COORDINATE FILE FOR SOLVATED SYSTEM ! CHARMM> ! CHECKS ARE DONE ON NUMBER OF MISSING ATOMS TO GUESS WHETHER FILE WAS ! CHARMM> ! PROCESSED CORRECTLY. EXAMINE OUTPUT FILE FOR POTENTIAL PROBLEMS! ! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHARMM> CHARMM> coor orie ORIENT THE COORDINATES TO ALIGN WITH AXIS MOMENTS 53508.43271118 12881.35434128 -15469.19132601 33294.96534834 -16668.94549320 36243.00401047 Transpose of the rotation matrix 0.516715 -0.456052 -0.724584 -0.503695 0.522429 -0.688011 0.692313 0.720475 0.040236 CENTER OF ATOMS BEFORE TRANSLATION 3.67483 19.35915 0.94151 AXIS OF ROTATION IS -0.704798 0.709007 0.023840 ANGLE IS 87.73 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> coor stat STATISTICS FOR 906 SELECTED ATOMS: XMIN = -17.723578 XMAX = 18.295086 XAVE = 0.000000 YMIN = -20.024844 YMAX = 11.676501 YAVE = 0.000000 ZMIN = -11.280407 ZMAX = 10.571868 ZAVE = 0.000000 WMIN = 0.000000 WMAX = 69.460000 WAVE = 14.251755 CHARMM> ! Orient the solute system at the origin and use the coor stat command CHARMM> ! to figure out the maximum dimension for solvation. CHARMM> CHARMM> Set min = 0 Parameter: MIN <- "0" CHARMM> Let min = mini ?xmin ?ymin RDCMND substituted energy or value "?XMIN" to "-17.7236" RDCMND substituted energy or value "?YMIN" to "-20.0248" Parameter: MIN <- "-20.0248" CHARMM> Let min = mini @min ?zmin Parameter: MIN -> "-20.0248" RDCMND substituted energy or value "?ZMIN" to "-11.2804" Parameter: MIN <- "-20.0248" CHARMM> Let min = Abs @min Parameter: MIN -> "-20.0248" Parameter: MIN <- "20.0248" CHARMM> CHARMM> Set max = 0 Parameter: MAX <- "0" CHARMM> Let max = maxi ?xmax ?ymax RDCMND substituted energy or value "?XMAX" to "18.2951" RDCMND substituted energy or value "?YMAX" to "11.6765" Parameter: MAX <- "18.2951" CHARMM> Let max = maxi @max ?zmax Parameter: MAX -> "18.2951" RDCMND substituted energy or value "?ZMAX" to "10.5719" Parameter: MAX <- "18.2951" CHARMM> Let max = maxi @max @min Parameter: MAX -> "18.2951" Parameter: MIN -> "20.0248" Parameter: MAX <- "20.0248" CHARMM> Calc maxD = @max Parameter: MAX -> "20.0248" Evaluating: 20.0248 Parameter: MAXD <- "20.0248" CHARMM> CHARMM> ! For a cubic volume the cube size should be about MAXD + CUTOFF CHARMM> CHARMM> calc L = 2 * ( @maxD + @cutoff ) Parameter: MAXD -> "20.0248" Parameter: CUTOFF -> "9" Evaluating: 2*(20.0248+9) Parameter: L <- "58.0496" CHARMM> CHARMM> ! For a truncated octahedron volume the size of the cubic box CHARMM> ! used to construct the solvent volume should be around CHARMM> ! 4 * (CUTOFF + MAXD) / Sqrt(3). CHARMM> CHARMM> if shape eq octahedral - CHARMM> calc L = @L * 2 / Sqrt(3) Parameter: L -> "58.0496" Comparing "OCTAHEDRAL" and "OCTAHEDRAL". IF test evaluated as true. Performing command Evaluating: 58.0496*2/SQRT(3) Parameter: L <- "67.0299" CHARMM> CHARMM> ! @L is the edgelength of a cubic box from which you want to CHARMM> ! cut the truncated octahedron to solvate the solute. Figure CHARMM> ! out whether its optimal to construct this from a basic CHARMM> ! water box of 125 or 216 molecules. CHARMM> CHARMM> goto bldbox CHARMM> ! Choose from two different boxsizes as basic building unit. CHARMM> ! minimize remainder! CHARMM> CHARMM> CHARMM> ! Edglength of cubic volume of 125 molecules CHARMM> Calc nboxsmall = int (@L / 15.5575) Parameter: L -> "67.0299" Evaluating: INT(67.0299/15.5575) Parameter: NBOXSMALL <- "4" CHARMM> calc remaindersmall = @L / 15.5575 - @nboxsmall Parameter: L -> "67.0299" Parameter: NBOXSMALL -> "4" Evaluating: 67.0299/15.5575-4 Parameter: REMAINDERSMALL <- "0.308527" CHARMM> if remaindersmall gt 0.0 Calc nboxsmall = @nboxsmall + 1 Parameter: NBOXSMALL -> "4" Comparing "0.308527" and "0.0". IF test evaluated as true. Performing command Evaluating: 4+1 Parameter: NBOXSMALL <- "5" CHARMM> Calc remaindersmall = @nboxsmall * 15.5575 - @L Parameter: NBOXSMALL -> "5" Parameter: L -> "67.0299" Evaluating: 5*15.5575-67.0299 Parameter: REMAINDERSMALL <- "10.7576" CHARMM> CHARMM> ! Edglength of cubic volume of 216 molecules CHARMM> Calc nboxbig = int (@L / 18.856) Parameter: L -> "67.0299" Evaluating: INT(67.0299/18.856) Parameter: NBOXBIG <- "3" CHARMM> calc remainderbig = @L / 18.856 - @nboxbig Parameter: L -> "67.0299" Parameter: NBOXBIG -> "3" Evaluating: 67.0299/18.856-3 Parameter: REMAINDERBIG <- "0.554831" CHARMM> if remainderbig gt 0.0 Calc nboxbig = @nboxbig + 1 Parameter: NBOXBIG -> "3" Comparing "0.554831" and "0.0". IF test evaluated as true. Performing command Evaluating: 3+1 Parameter: NBOXBIG <- "4" CHARMM> Calc remainderbig = @nboxbig * 18.856 - @L Parameter: NBOXBIG -> "4" Parameter: L -> "67.0299" Evaluating: 4*18.856-67.0299 Parameter: REMAINDERBIG <- "8.3941" CHARMM> CHARMM> set size 15.5575 Parameter: SIZE <- "15.5575" CHARMM> set nwat 125 Parameter: NWAT <- "125" CHARMM> Set nbox = @nboxsmall Parameter: NBOXSMALL -> "5" Parameter: NBOX <- "5" CHARMM> CHARMM> if remainderbig gt @remaindersmall goto notbig Parameter: REMAINDERSMALL -> "10.7576" Comparing "8.3941" and "10.7576". IF test evaluated as false. Skipping command CHARMM> Set nbox = @nboxbig Parameter: NBOXBIG -> "4" Parameter: NBOX <- "4" CHARMM> set size 18.856 Parameter: SIZE <- "18.856" CHARMM> set nwat 216 Parameter: NWAT <- "216" CHARMM> label notbig CHARMM> CHARMM> calc n (@nbox - 1) / 2 Parameter: NBOX -> "4" Evaluating: (4-1)/2 Parameter: N <- "1.5" CHARMM> CHARMM> ! Build a big cube to surround solute CHARMM> prnlev 0 node 0 **** Warning **** The following extraneous characters were found while command processing in MISCOM OPNLGU> Unit already open. The old file will be closed first. **** Warning **** The following extraneous characters were found while command processing in MISCOM NODE 0 CHARMM> coor stats STATISTICS FOR42378 SELECTED ATOMS: XMIN = -38.305080 XMAX = 38.134320 XAVE = 0.166966 YMIN = -38.319840 YMAX = 38.475010 YAVE = -0.073570 ZMIN = -38.234810 ZMAX = 38.305530 ZAVE = 0.114556 WMIN = 0.000000 WMAX = 69.460000 WAVE = 0.304689 CHARMM> goto donebldbox CHARMM> CHARMM> ! NOTE ASSUMPTION THAT ONLY SOLVENT SEGIDS BEGIN WITH W CHARMM> define solvent select segid w* end SELRPN> 41472 atoms have been selected out of 42378 CHARMM> CHARMM> Calc size = @size * @nbox Parameter: SIZE -> "18.856" Parameter: NBOX -> "4" Evaluating: 18.856*4 Parameter: SIZE <- "75.424" CHARMM> if shape ne cubic set size = @L Parameter: L -> "67.0299" Comparing "OCTAHEDRAL" and "CUBIC". IF test evaluated as true. Performing command Parameter: SIZE <- "67.0299" CHARMM> Set 7 = @size Parameter: SIZE -> "67.0299" Parameter: 7 <- "67.0299" CHARMM> set 8 = @7 Parameter: 7 -> "67.0299" Parameter: 8 <- "67.0299" CHARMM> set 9 = @7 Parameter: 7 -> "67.0299" Parameter: 9 <- "67.0299" CHARMM> set theta = 109.4712206344907 Parameter: THETA <- "109.4712206344907" CHARMM> set xtl = @7 Parameter: 7 -> "67.0299" Parameter: XTL <- "67.0299" CHARMM> Calc xtl = sqrt (3) * @xtl / 2 Parameter: XTL -> "67.0299" Evaluating: SQRT(3)*67.0299/2 Parameter: XTL <- "58.0496" CHARMM> CHARMM> if shape ne cubic goto makeshape Comparing "OCTAHEDRAL" and "CUBIC". IF test evaluated as true. Performing command CHARMM> prnlev 0 node 0 **** Warning **** The following extraneous characters were found while command processing in MISCOM GTNBCT> CUTNB,CTOFNB,CTONNB= 3.0 3.0 3.0 ***** LEVEL 1 WARNING FROM ***** ***** CUTNB,CTOFNB,CTONNB are not in correct order. ****************************************** BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 2 **** Warning **** The following extraneous characters were found while command processing in MISCOM NODE 0 CHARMM> delete atom select .byres. ( xout .or. yout .or. zout ) end SELRPN> 26973 atoms have been selected out of 42378 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 8991 residues deleted. Message from MAPIC: 8 segments deleted. DELTIC:26973 bonds deleted DELTIC: 8991 angles deleted DELTIC: 8991 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 57 Number of residues = 4894 Number of atoms = 15405 Number of groups = 5092 Number of bonds = 15418 Number of angles = 6491 Number of dihedrals = 2440 Number of impropers = 159 Number of HB acceptors = 4925 Number of HB donors = 119 Number of NB exclusions = 0 Total charge = 4.00000 CHARMM> if crystal ne true goto doneshape Comparing "TRUE" and "TRUE". IF test evaluated as false. Skipping command CHARMM> Calc onethird = 1.0000 / 3.0000 Evaluating: 1.0000/3.0000 Parameter: ONETHIRD <- "0.333333" CHARMM> Calc twothird = 2.0000 / 3.0000 Evaluating: 2.0000/3.0000 Parameter: TWOTHIRD <- "0.666667" CHARMM> CHARMM> format (f15.8) CHARMM> coor rotate matrix CORMAN> @twothird -@onethird -@twothird ! image -> crystal Parameter: TWOTHIRD -> "0.666667" Parameter: ONETHIRD -> "0.333333" Parameter: TWOTHIRD -> "0.666667" CORMAN> -@onethird @twothird -@twothird ! image -> crystal Parameter: ONETHIRD -> "0.333333" Parameter: TWOTHIRD -> "0.666667" Parameter: TWOTHIRD -> "0.666667" CORMAN> @twothird @twothird @onethird ! image -> crystal Parameter: TWOTHIRD -> "0.666667" Parameter: TWOTHIRD -> "0.666667" Parameter: ONETHIRD -> "0.333333" ROTATION MATRIX 0.666667 -0.333333 -0.666667 -0.333333 0.666667 -0.666667 0.666667 0.666667 0.333333 AXIS OF ROTATION IS -0.707107 0.707107 0.000000 ANGLE IS 70.53 SELECTED COORDINATES ROTATED IN THE MAIN SET. CHARMM> CHARMM> goto doneshape CHARMM> CHARMM> goto writesolvent CHARMM> define solvent select segid w* .and. .not. hydrogen end SELRPN> 4833 atoms have been selected out of 15405 CHARMM> set nwat ?nsel RDCMND substituted energy or value "?NSEL" to "4833" Parameter: NWAT <- "4833" CHARMM> if shape eq cubic goto writecube Comparing "OCTAHEDRAL" and "CUBIC". IF test evaluated as false. Skipping command CHARMM> if crystal eq true open unit 1 write form name xtl_oct@nwat.crd Parameter: NWAT -> "4833" Comparing "TRUE" and "TRUE". IF test evaluated as true. Performing command VOPEN> Attempting to open::xtl_oct4833.crd:: OPNLGU> Unit 1 opened for WRITE access to xtl_oct4833.crd CHARMM> if crystal ne true open unit 1 write form name img_oct@nwat.crd Parameter: NWAT -> "4833" Comparing "TRUE" and "TRUE". IF test evaluated as false. Skipping command CHARMM> write coor card unit 1 select segid w* end RDTITL> * COORDINATES FOR A TRUNCATED OCTAHEDRON CONSTRUCTED FROM RDTITL> * A CUBIC VOLUME OF WATER MOLECULES IN A PARALLELPIPED OF RDTITL> * DIMENSION 67.0299 AX67.0299 AX67.0299 A ON A SIDE. THERE ARE 4833 MOLECULES RDTITL> * IN THIS FILE. RDTITL> * IF KEY FOR CRYSTAL = TRUE USE: RDTITL> * SET THETA = 109.4712206344907 RDTITL> * CRYSTAL DEFINE OCTA 58.0496 58.0496 58.0496 109.4712206344907 109.4712206344907 109.4712206344907 RDTITL> * SELRPN> 14499 atoms have been selected out of 15405 NOTE: A SELECTED SUBSET OF ATOMS WILL BE USED VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> goto donewrite CHARMM> CHARMM> label deleteoverlapping CHARMM> define solute select .not. segid w* end SELRPN> 906 atoms have been selected out of 15405 CHARMM> ! Remove water overlaps with solute system CHARMM> delete atom sele .byres. ( segid w* .and. type OH2 .and. - CHARMM> (( solute .and. .not. hydrogen ) - CHARMM> .around. 2.8 )) end SELRPN> 1089 atoms have been selected out of 15405 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 363 residues deleted. DELTIC: 1089 bonds deleted DELTIC: 363 angles deleted DELTIC: 363 acceptors deleted PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 57 Number of residues = 4531 Number of atoms = 14316 Number of groups = 4729 Number of bonds = 14329 Number of angles = 6128 Number of dihedrals = 2440 Number of impropers = 159 Number of HB acceptors = 4562 Number of HB donors = 119 Number of NB exclusions = 0 Total charge = 4.00000 CHARMM> CHARMM> define solvent select segid w* .and. .not. hydrogen end SELRPN> 4470 atoms have been selected out of 14316 CHARMM> set nwat ?nsel RDCMND substituted energy or value "?NSEL" to "4470" Parameter: NWAT <- "4470" CHARMM> if shape eq cubic open unit 1 write form name @pdbfile_solv-cube.crd Parameter: PDBFILE -> "1FSC" Comparing "OCTAHEDRAL" and "CUBIC". IF test evaluated as false. Skipping command CHARMM> if shape eq octahedral open unit 1 write form name @pdbfile_solv-octa.crd Parameter: PDBFILE -> "1FSC" Comparing "OCTAHEDRAL" and "OCTAHEDRAL". IF test evaluated as true. Performing command VOPEN> Attempting to open::1fsc_solv-octa.crd:: OPNLGU> Unit 1 opened for WRITE access to 1fsc_solv-octa.crd CHARMM> CHARMM> write coor card unit 1 RDTITL> * X-RAY STRUCTURE OF SOLUTE SYSTEM 1FSC SOLVATED IN A OCTAHEDRAL VOLUME CONSTRUCTED RDTITL> * FROM A CUBE OF EDGELENGTH 67.0299 A. VOLUME CONTAINS 4470 WATER MOLECULES. RDTITL> * IF VOLUME SHAPE IS CUBIC, USE DIMENSIONS 67.0299. RDTITL> * IF VOLUME SHAPE IS OCTAHEDRAL USE BASIC DIMENSIONS OF 67.0299 X 67.0299 X 67.0299 AND RDTITL> * A TETRAHEDRAL ANGLE WITH OCTAHEDRAL SYMMETRY FOR CRYSTAL FACILITY RDTITL> * OR USE IMAGE FACILITY WITH DIMENSIONS JUST NOTED. RDTITL> * CRYSTAL FACILITY LOGICAL FLAG = TRUE, USE: RDTITL> * SET THETA = 109.4712206344907 RDTITL> * CRYSTAL DEFINE OCTA 58.0496 58.0496 58.0496 109.4712206344907 109.4712206344907 109.4712206344907 RDTITL> * VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> close unit 1 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> if shape eq cubic open unit 1 write form name @pdbfile_solv-cube.pdb Parameter: PDBFILE -> "1FSC" Comparing "OCTAHEDRAL" and "CUBIC". IF test evaluated as false. Skipping command CHARMM> if shape eq octahedral open unit 1 write form name @pdbfile_solv-octa.pdb Parameter: PDBFILE -> "1FSC" Comparing "OCTAHEDRAL" and "OCTAHEDRAL". IF test evaluated as true. Performing command VOPEN> Attempting to open::1fsc_solv-octa.pdb:: OPNLGU> Unit 1 opened for WRITE access to 1fsc_solv-octa.pdb CHARMM> write coor pdb unit 1 RDTITL> CLOSE UNIT 1 RDTITL> No title read. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> if shape eq cubic open unit 1 write form name @pdbfile_solv-cube.psf Parameter: PDBFILE -> "1FSC" Comparing "OCTAHEDRAL" and "CUBIC". IF test evaluated as false. Skipping command CHARMM> if shape eq octahedral open unit 1 write form name @pdbfile_solv-octa.psf Parameter: PDBFILE -> "1FSC" Comparing "OCTAHEDRAL" and "OCTAHEDRAL". IF test evaluated as true. Performing command VOPEN> Attempting to open::1fsc_solv-octa.psf:: OPNLGU> Unit 1 opened for WRITE access to 1fsc_solv-octa.psf CHARMM> write psf card unit 1 RDTITL> CLOSE UNIT 1 RDTITL> No title read. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> set theta = 90.0 Parameter: THETA <- "90.0" CHARMM> if shape eq octahedral set theta = 109.4712206344907 Comparing "OCTAHEDRAL" and "OCTAHEDRAL". IF test evaluated as true. Performing command Parameter: THETA <- "109.4712206344907" CHARMM> CHARMM> open unit 1 write form name @pdbfile_dimens.stream Parameter: PDBFILE -> "1FSC" VOPEN> Attempting to open::1fsc_dimens.stream:: OPNLGU> Unit 1 opened for WRITE access to 1fsc_dimens.stream CHARMM> write title unit 1 RDTITL> ** STREAM FILE TO ESTABLISH DIMENSIONS FOR RDTITL> ** DYNAMICS SIMULATION OF 1FSC USING PBCS RDTITL> ** RDTITL> * SET TOPPAR = "$toppar" RDTITL> * SET PDBFILE = 1FSC RDTITL> * SET SHAPE = OCTAHEDRAL RDTITL> * SET CRYSTAL = TRUE RDTITL> * SET CUTOFF = 9 RDTITL> * SET NWAT = 4470 RDTITL> * SET SIZE = 67.0299 RDTITL> * SET THETA = 109.4712206344907 RDTITL> CHARMM> CHARMM> stop VCLOSE: Closing unit 1 with status "KEEP" $$$$$$ New timer profile $$$$$ Nonbond force 63.29876 Other: 0.00000 Bond energy 0.72503 Other: 0.00000 Angle energy 2.81950 Other: 0.00000 Dihedral energy 6.07200 Other: 0.00000 Energy time 73.68979 Other: 0.77451 Dynamics total 73.68979 Other: 0.00000 Total time 338.65556 Other: 264.96577 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 795772 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL 1 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 4224 MAXIMUM SPACE USED IS 3541316 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10175198 NEXT: 10179423 PRINHP> ADDRESS: 10179423 LENGTH: 60578 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 5.88 MINUTES CPU TIME: 5.64 MINUTES