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 5/25/ 0 at 11: 7:23 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 "begin=1" Parameter: BEGIN <- "1" Processing passed argument "end=8" Parameter: END <- "8" Processing passed argument "task=atomrms" Parameter: TASK <- "ATOMRMS" RDTITL> * CORREL RDTITL> * CHARMM> CHARMM> if @?task eq 0 goto deadformat Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> CHARMM> if @?pdbfile eq 0 goto iamdead Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> CHARMM> stream @pdbfile_dimens.stream Parameter: PDBFILE -> "1FSC" VOPEN> Attempting to open::1fsc_dimens.stream:: OPNLGU> Unit 99 opened for READONLY access to 1fsc_dimens.stream INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * STREAM FILE TO ESTABLISH DIMENSIONS FOR RDTITL> * DYNAMICS SIMULATION OF 1FSC USING PBCS RDTITL> * Parameter: IN1 <- "" CHARMM> SET TOPPAR = "$toppar" Parameter: TOPPAR <- ""$toppar"" CHARMM> SET PDBFILE = 1FSC Parameter: PDBFILE <- "1FSC" CHARMM> SET SHAPE = OCTAHEDRAL Parameter: SHAPE <- "OCTAHEDRAL" CHARMM> SET CRYSTAL = TRUE Parameter: CRYSTAL <- "TRUE" CHARMM> SET CUTOFF = 9 Parameter: CUTOFF <- "9" CHARMM> SET NWAT = 4470 Parameter: NWAT <- "4470" CHARMM> SET SIZE = 67.0299 Parameter: SIZE <- "67.0299" CHARMM> SET THETA = 109.4712206344907 Parameter: THETA <- "109.4712206344907" VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> !********************************************************* CHARMM> ! get parameters set for this run CHARMM> !********************************************************* CHARMM> ! CHARMM> goto getparams CHARMM> !********************************************************* CHARMM> ! get parameters set for this run CHARMM> !********************************************************* CHARMM> ! CHARMM> CHARMM> if @?toppar eq 0 set toppar = "$toppar" Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> if @?T eq 0 set T = 298 Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: T <- "298" CHARMM> if @?begin eq 0 set begin = 1 Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> if @?end eq 0 set end = 10 Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> if @?current eq 0 set current = 1 Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: CURRENT <- "1" 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 "1" and "0". IF test evaluated as false. Skipping command CHARMM> if @?status eq 0 set status start Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: STATUS <- "START" CHARMM> if @?water eq 0 set water false Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: WATER <- "FALSE" CHARMM> CHARMM> ! Dimension of the solvent volume CHARMM> Calc 7 = @size * 1.005 ! Initially set boxsize slightly larger for CPT equilibration Parameter: SIZE -> "67.0299" Evaluating: 67.0299*1.005 Parameter: 7 <- "67.3651" CHARMM> if @shape ne octahedral goto sizeok Parameter: SHAPE -> "OCTAHEDRAL" Comparing "OCTAHEDRAL" and "OCTAHEDRAL". IF test evaluated as false. Skipping command CHARMM> if @crystal eq true calc 7 = @7 * sqrt(3) / 2. Parameter: CRYSTAL -> "TRUE" Parameter: 7 -> "67.3651" Comparing "TRUE" and "TRUE". IF test evaluated as true. Performing command Evaluating: 67.3651*SQRT(3)/2. Parameter: 7 <- "58.3399" CHARMM> label sizeok CHARMM> set 8 @7 Parameter: 7 -> "58.3399" Parameter: 8 <- "58.3399" CHARMM> set 9 @8 Parameter: 8 -> "58.3399" Parameter: 9 <- "58.3399" CHARMM> CHARMM> ! Set-up cutoffs for non-bonded list and energy calculations CHARMM> Calc cutoff = @cutoff + 1 ! Add additional 1A to cutoff from build Parameter: CUTOFF -> "9" Evaluating: 9+1 Parameter: CUTOFF <- "10" CHARMM> set ctofnb = @cutoff Parameter: CUTOFF -> "10" Parameter: CTOFNB <- "10" CHARMM> Calc ctofnb = @ctofnb - 1.5 Parameter: CTOFNB -> "10" Evaluating: 10-1.5 Parameter: CTOFNB <- "8.5" CHARMM> set ctonnb = @ctofnb Parameter: CTOFNB -> "8.5" Parameter: CTONNB <- "8.5" CHARMM> Calc ctonnb = @ctonnb - 1.0 Parameter: CTONNB -> "8.5" Evaluating: 8.5-1.0 Parameter: CTONNB <- "7.5" CHARMM> CHARMM> goto doneparams CHARMM> CHARMM> !********************************************************* CHARMM> ! get topology and force field for this run CHARMM> !********************************************************* CHARMM> ! CHARMM> CHARMM> !prnlev 0 node 0 CHARMM> wrnlev 0 CHARMM> open unit 1 read form name @toppar/top_all22_prot.inp Parameter: TOPPAR -> ""$toppar"" VOPEN> Attempting to open::../top_all22_prot.inp:: OPNLGU> Unit 1 opened for READONLY access to ../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::../par_all22_prot.inp:: OPNLGU> Unit 1 opened for READONLY access to ../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> * 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 CHARMM> wrnlev 2 CHARMM> CHARMM> CHARMM> !********************************************************* CHARMM> ! get psf for this system CHARMM> ! This psf does not have the solvent CHARMM> !********************************************************* CHARMM> ! CHARMM> open unit 1 read form name @pdbfile.psf Parameter: PDBFILE -> "1FSC" VOPEN> Attempting to open::1fsc.psf:: OPNLGU> Unit 1 opened for READONLY access to 1fsc.psf CHARMM> read psf card unit 1 MAINIO> Protein structure file being read from unit 1. TITLE> * THIS IS A GENERAL TEMPLATE SCRIPT TO CREATE A SOLVATED TITLE> * SIMULATION "box" USING PERIODIC BOUNDARIES WITH A FEW SPECIFIC VOLUMES. TITLE> * THE SCRIPT WILL GENERATE, MINIMIZE (OR ALTERNATIVELY READ IN A PSF TITLE> * FILE FOR A SOLUTE SYSTEM ALREADY GENERATED) A SOLUTE SYSTEM IN A: TITLE> * 1) CUBIC VOLUME W/ IMAGES OR CRYSTAL TITLE> * 2) TRUNCATED OCTAHEDRAL BOX W/ IMAGES TITLE> * 3) TRUNCATED OCTAHEDRAL BOX W/ CRYSTAL (REORIENTED FROM IMAGES) TITLE> *** TITLE> * REQUIRED FILES: TOP_ALL22_PROT.INP, PAR_ALL22_PROT.INP TITLE> ** OCTA.IMG, TIP125.CRD, TIP216.CRD TITLE> * DATE: 5/24/ 0 16:15:11 CREATED BY USER: crowley TITLE> * 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 CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> CHARMM> !********************************************************* CHARMM> ! Add water CHARMM> !********************************************************* CHARMM> read sequ tip3 @nwat Parameter: NWAT -> "4470" CHARMM> generate wat setup noangl nodihe NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 2 has been generated. Its identifier is WAT . PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 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> goto @task Parameter: TASK -> "ATOMRMS" CHARMM> !********************************************************* CHARMM> ! Atom Average rms CHARMM> !********************************************************* CHARMM> if @water eq true goto atrmswat Parameter: WATER -> "FALSE" Comparing "FALSE" and "TRUE". IF test evaluated as false. Skipping command CHARMM> delete atom sele resn TIP3 end SELRPN> 13410 atoms have been selected out of 14316 Message from MAPIC: Atom numbers are changed. Message from MAPIC: 4470 residues deleted. Message from MAPIC: 1 segments deleted. DELTIC:13410 bonds deleted DELTIC: 4470 angles deleted DELTIC: 4470 acceptors 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 CHARMM> set avgnam @pdbfile_e@begin-@end_nowat.avgcrd Parameter: PDBFILE -> "1FSC" Parameter: BEGIN -> "1" Parameter: END -> "8" Parameter: AVGNAM <- "1FSC_E1-8_NOWAT.AVGCRD" CHARMM> open unit 30 unform read name @pdbfile_e@begin-@end_nowat.crd Parameter: PDBFILE -> "1FSC" Parameter: BEGIN -> "1" Parameter: END -> "8" VOPEN> Attempting to open::1fsc_e1-8_nowat.crd:: OPNLGU> Unit 30 opened for READONLY access to 1fsc_e1-8_nowat.crd CHARMM> open unit 31 form write name @avgnam Parameter: AVGNAM -> "1FSC_E1-8_NOWAT.AVGCRD" VOPEN> Attempting to open::1fsc_e1-8_nowat.avgcrd:: OPNLGU> Unit 31 opened for WRITE access to 1fsc_e1-8_nowat.avgcrd CHARMM> open unit 32 form write name @pdbfile_e@begin-@end_nowat.avgdmb Parameter: PDBFILE -> "1FSC" Parameter: BEGIN -> "1" Parameter: END -> "8" VOPEN> Attempting to open::1fsc_e1-8_nowat.avgdmb:: OPNLGU> Unit 32 opened for WRITE access to 1fsc_e1-8_nowat.avgdmb CHARMM> coor dyna comp firstu 30 nunit 1 READING TRAJECTORY FROM UNIT 30 NUMBER OF COORDINATE SETS IN FILE: 800 NUMBER OF PREVIOUS DYNAMICS STEPS: 100 FREQUENCY FOR SAVING COORDINATES: 100 NUMBER OF STEPS FOR CREATION RUN: 80000 TITLE> * INITIAL DYNAMICS FOR 1FSC. TITLE> * DYNAMICS INITIATED FROM COOLED STRUCTURE AND HEATED TO 298K OVER TITLE> * 50K STEPS (100PS) OF DYNAMICS. PRODUCTION FOR 1 20PS WINDOW. TITLE> * HARMONIC FORCE RESTRAINTS APPLIED DURING THE FIRST 20PS USING A FORCE TITLE> * CONSTANT OF 5*MASS. TITLE> * DATE: 5/25/ 0 10:51: 3 CREATED BY USER: crowley TITLE> * ***** WARNING ***** SKIP= 1 WAS NOT A MULTIPLE OF THE FILE INTERVAL= 100 IT HAS BEEN RESET TO 100 ***** WARNING ***** BEGIN= 0 Was not specified. It has been set to: 100 800 CORD RECORDS READ FROM 1 UNITS STARTING WITH UNIT 30 RUNNING FROM STEP 100 TO 80000 SKIPPING 100 STEPS BETWEEN RECORDS Time step was 4.0909655E-02 AKMA time units. CHARMM> write coor comp card unit 31 RDTITL> WRITE COOR COMP DUMB UNIT 32 RDTITL> No title read. VCLOSE: Closing unit 31 with status "KEEP" CHARMM> write coor comp dumb unit 32 RDTITL> CLOSE UNIT 30 RDTITL> No title read. CHARMM> close unit 30 VCLOSE: Closing unit 30 with status "KEEP" CHARMM> close unit 31 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> close unit 32 VCLOSE: Closing unit 32 with status "KEEP" CHARMM> CHARMM> goto extractrms CHARMM> !********************************************************* CHARMM> ! fix rms file for plotting CHARMM> !********************************************************* CHARMM> ! CHARMM> CHARMM> system "/bin/rm -f rms_fnam rms.csh awk.file" Invoking: /bin/rm -f rms_fnam rms.csh awk.file CHARMM> system "echo 'BEGIN {header = 1 }' > awk.file" Invoking: echo 'BEGIN {header = 1 }' > awk.file CHARMM> system "echo '{if ( header == 1 ){' >> awk.file" Invoking: echo '{if ( header == 1 ){' >> awk.file CHARMM> system "echo 'if ($1 == "\*") header = 1;' >> awk.file" Invoking: echo 'if ($1 == "\*") header = 1;' >> awk.file CHARMM> system "echo ' else header = 0; } ' >> awk.file" Invoking: echo ' else header = 0; } ' >> awk.file CHARMM> system "echo 'else print $1, $10; }' >> awk.file" Invoking: echo 'else print $1, $10; }' >> awk.file CHARMM> CHARMM> system "echo @AVGNAM | awk '{print tolower($1)}' >rms_fnam `" Parameter: AVGNAM -> "1FSC_E1-8_NOWAT.AVGCRD" Invoking: echo 1FSC_E1-8_NOWAT.AVGCRD | awk '{print tolower($1)}' >rms_fnam ` CHARMM> system "echo ' set fnam=`cat rms_fnam`; set fnam=$fnam:r ; /bin/rm -f $fnam.rms ' >> rms.csh" Invoking: echo ' set fnam=`cat rms_fnam`; set fnam=$fnam:r ; /bin/rm -f $fnam.rms ' >> rms.csh CHARMM> system "echo 'awk -f awk.file $fnam.avgcrd > $fnam.rms ' >> rms.csh" Invoking: echo 'awk -f awk.file $fnam.avgcrd > $fnam.rms ' >> rms.csh CHARMM> system "csh rms.csh" Invoking: csh rms.csh CHARMM> system "/bin/rm -f rms_fnam rms.csh awk.file" Invoking: /bin/rm -f rms_fnam rms.csh awk.file CHARMM> CHARMM> goto doneextrms CHARMM> stop $$$$$$ New timer profile $$$$$ Total time 2.30160 Other: 0.00000 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47526 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 100692 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 4.00 SECONDS CPU TIME: 2.30 SECONDS