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 11:38: 2 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=timerms" Parameter: TASK <- "TIMERMS" 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 -> "TIMERMS" CHARMM> !********************************************************* CHARMM> ! time series of average rms CHARMM> !********************************************************* CHARMM> if @water eq true goto trmswat 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> 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> traj iread 30 TRAJ: INITIATING READ OF A TRAJECTORY, OPTIONS; FIRSTU = 30 NUNIT = 1 SKIP = 1 CHARMM> traj read 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 CHARMM> close unit 30 VCLOSE: Closing unit 30 with status "KEEP" 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 40 form write name @pdbfile_e@begin-@end_nowat.trms_dumb Parameter: PDBFILE -> "1FSC" Parameter: BEGIN -> "1" Parameter: END -> "8" VOPEN> Attempting to open::1fsc_e1-8_nowat.trms_dumb:: OPNLGU> Unit 40 opened for WRITE access to 1fsc_e1-8_nowat.trms_dumb CHARMM> open unit 41 form write name @pdbfile_e@begin-@end_nowat.trms_card" Parameter: PDBFILE -> "1FSC" Parameter: BEGIN -> "1" Parameter: END -> "8" VOPEN> Attempting to open::1fsc_e1-8_nowat.trms_card:: OPNLGU> Unit 41 opened for WRITE access to 1fsc_e1-8_nowat.trms_card CHARMM> coor copy comp SELECTED COORDINATES COPIED TO THE COMPARISON SET. CHARMM> CHARMM> correl maxt 1000 maxseries 100 maxatoms 1500 bycb - CHARMM> eps 1.0 cutnb @cutoff cutim @cutoff ctofnb @ctofnb ctonnb @ctonnb vswi - CHARMM> Ewald kappa 0.320 pmEwald order 4 fftx 64 ffty 64 fftz 64 Parameter: CUTOFF -> "10" Parameter: CUTOFF -> "10" Parameter: CTOFNB -> "8.5" Parameter: CTONNB -> "7.5" PME: Total heap storage needed = 1122510 Fill Ewald table: Number of points= 10000 EWXmin= 0.000000 EWXmax= 2.880000 Fill ERFC table: linear inter has rms error=0.545846D-08 Maximum error=0.100370D-07 Fill ERFC table: cubic spline has rms error=0.135935D-11 Maximum error=0.337042D-11 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd EWALd CUTNB = 10.000 CTEXNB =999.000 CTONNB = 7.500 CTOFNB = 8.500 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 EWALD OPTIONS: KAPPA = 0.320 KMAX = 5 KSQMAX = 27 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 0 ATOM PAIRS AND 0 GROUP PAIRS == IMAGES === SPACE FOR 0 ATOM PAIRS AND 0 GROUP PAIRS ========================================= TRIAL run of list........... ========================================= Using Image CUBE search 4 3 4 10.00000000000000 Using Image CUBE search 4 3 4 10.00000000000000 NBNDGCM found: 95885 atom pairs 0 image atom pairs **** Warning **** The following extraneous characters were found while command processing in CORREL CUTIM 10 CORREL> enter rms rms orient CORREL> traj first 30 nunit 1 The following time series will be filled: RMS 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. 1 Series "RMS " Average = 1.349849 rms Fluctuation = 0.292983 CORREL> show all NSER: 1 NAMES: RMS TOTALS: 800 AVERAGE: 1.349849 FLUCT: 0.292983 VECCOD: 1 CLASS: RMS VELCOD: 0 SKIP: 100 DELTA: 0.002000 OFFST: 0.200000 GECOD: 2 VALUE: 0.000000 Atom pointers for all time series: SERPT: 1 SERNQ: 0 QAT : CORREL> write rms unit 40 dumb RDTITL> WRITE RMS UNIT 41 CARD RDTITL> No title read. VCLOSE: Closing unit 40 with status "KEEP" CORREL> write rms unit 41 card RDTITL> END RDTITL> No title read. VCLOSE: Closing unit 41 with status "KEEP" CORREL> end CHARMM> CHARMM> system "grep -v "^*" 1fsc_e1-8_nowat.trms_card | tail +12 > 1fsc_e1-8_nowat.trms" Invoking: grep -v "^*" 1fsc_e1-8_nowat.trms_card | tail +12 > 1fsc_e1-8_nowat.trms CHARMM> CHARMM> stop VCLOSE: Closing unit 30 with status "KEEP" $$$$$$ New timer profile $$$$$ Total time 2.86205 Other: 0.00000 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47526 STACK CURRENTLY IN USE IS 0 NO WARNINGS WERE ISSUED HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 10978 MAXIMUM SPACE USED IS 414966 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10066114 NEXT: 10069843 PRINHP> ADDRESS: 10069843 LENGTH: 162430 NEXT: 10239521 PRINHP> ADDRESS: 10239521 LENGTH: 478 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 3.00 SECONDS CPU TIME: 2.86 SECONDS