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 5/12/ 0 at 9:58:59 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 "crystal=true" Parameter: CRYSTAL <- "TRUE" Processing passed argument "shape=octahedral" Parameter: SHAPE <- "OCTAHEDRAL" RDTITL> * THIS IS A GENERAL TEMPLATE SCRIPT TO EQUILIBRATE A SOLVATED RDTITL> * SIMULATION "box" USING PERIODIC BOUNDARIES WITH A FEW SPECIFIC VOLUMES. RDTITL> * THE SCRIPT WILL READ IN A PSF FILE FOR A SOLUTE SYSTEM ALREADY GENERATED RDTITL> * IN A: RDTITL> * 1) CUBIC VOLUME W/ CRYSTAL RDTITL> * 2) TRUNCATED OCTAHEDRAL BOX W/ CRYSTAL (REORIENTED FROM IMAGES) RDTITL> * 3) CARRY-OUT AN EQUILIBRATION NPT DYNAMICS RUN W/ PME RDTITL> *** RDTITL> * REQUIRED FILES: TOP_ALL22_PROT.INP, PAR_ALL22_PROT.INP RDTITL> ** RHOMBA.XTL, OUTPUT FROM PROTEIN-GENERATE_SOLVATE.INP RDTITL> * CHARMM> 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 ($toppar) ==> path to parameter and topology files CHARMM> !** CHARMM> !* pdbfile (...) ==> name of charmm (crd) coordinate file containing CHARMM> !** coordinates of the solvated system CHARMM> !** (pdbfile_solv-cube(octa).crd) CHARMM> !** and the pre-generated psf file (pdbfile.psf)) CHARMM> !* shape (cubic) ==> variable specifying whether truncated octahedral or CHARMM> !** cubic volume used (octahedral/cubic) CHARMM> !* crystal (false) ==> logical variable true/false specifying whether CHARMM> !** to use crystal orientation of simulation volume CHARMM> !* cutoff (9) ==> value of cutoff to be used in establishing how CHARMM> !** far images are to be from volume "edges", often set CHARMM> !** at or near nonbonded list cutoff value CHARMM> !* T (298) ==> Temperature for run. Default 298K. CHARMM> !** at or near nonbonded list cutoff value CHARMM> !* begin (1) ==> Window to begin this production run from CHARMM> !** CHARMM> !* end (10) ==> Window to end this production run at CHARMM> !** CHARMM> !* current (begin) ==> Window last run CHARMM> !** CHARMM> ! CHARMM> CHARMM> if @?pdbfile eq 0 goto iamdead Comparing "1" and "0". IF test evaluated as false. Skipping command CHARMM> CHARMM> stream @pdbfile_dimens.stream Parameter: PDBFILE -> "1FSC" VOPEN> Attempting to open::1fsc_dimens.stream:: OPNLGU> Unit 99 opened for READONLY access to 1fsc_dimens.stream INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * STREAM FILE TO ESTABLISH DIMENSIONS FOR RDTITL> * DYNAMICS SIMULATION OF 1FSC USING PBCS RDTITL> * Parameter: IN1 <- "" CHARMM> SET TOPPAR = "$toppar" Parameter: TOPPAR <- ""$toppar"" CHARMM> SET PDBFILE = 1FSC Parameter: PDBFILE <- "1FSC" CHARMM> SET SHAPE = OCTAHEDRAL Parameter: SHAPE <- "OCTAHEDRAL" CHARMM> SET CRYSTAL = TRUE Parameter: CRYSTAL <- "TRUE" CHARMM> SET CUTOFF = 9 Parameter: CUTOFF <- "9" CHARMM> SET NWAT = 4470 Parameter: NWAT <- "4470" CHARMM> SET SIZE = 67.0299 Parameter: SIZE <- "67.0299" CHARMM> SET THETA = 109.4712206344907 Parameter: THETA <- "109.4712206344907" VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> if @?toppar eq 0 set toppar = "$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 "0" and "0". IF test evaluated as true. Performing command Parameter: BEGIN <- "1" CHARMM> if @?end eq 0 set end = 10 Comparing "0" and "0". IF test evaluated as true. Performing command Parameter: END <- "10" 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> 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> set 8 @7 Parameter: 7 -> "67.3651" Parameter: 8 <- "67.3651" CHARMM> set 9 @8 Parameter: 8 -> "67.3651" Parameter: 9 <- "67.3651" 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> prnlev 0 CHARMM> wrnlev 2 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: 5/11/ 0 21:37:30 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> 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> if shape eq cubic open unit 1 read 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 read 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 READONLY access to 1fsc_solv-octa.crd CHARMM> read coor card unit 1 SPATIAL COORDINATES BEING READ FROM UNIT 1 TITLE> * X-RAY STRUCTURE OF SOLUTE SYSTEM 1FSC SOLVATED IN A OCTAHEDRAL VOLUME CONSTRUC TITLE> * FROM A CUBE OF EDGELENGTH 67.0299 A. VOLUME CONTAINS 4470 WATER MOLECULES. TITLE> * IF VOLUME SHAPE IS CUBIC, USE DIMENSIONS 67.0299. TITLE> * IF VOLUME SHAPE IS OCTAHEDRAL USE BASIC DIMENSIONS OF 67.0299 X 67.0299 X 67.0 TITLE> * A TETRAHEDRAL ANGLE WITH OCTAHEDRAL SYMMETRY FOR CRYSTAL FACILITY TITLE> * OR USE IMAGE FACILITY WITH DIMENSIONS JUST NOTED. TITLE> * CRYSTAL FACILITY LOGICAL FLAG = TRUE, USE: TITLE> * SET THETA = 109.4712206344907 TITLE> * CRYSTAL DEFINE OCTA 67.0299 67.0299 67.0299 109.4712206344907 109.471220634490 TITLE> * DATE: 5/11/ 0 21:18:27 CREATED BY USER: CROWLEY TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> if shape ne cubic goto doocta Comparing "OCTAHEDRAL" and "CUBIC". IF test evaluated as true. Performing command CHARMM> if shape ne octahedral goto donextl Comparing "OCTAHEDRAL" and "OCTAHEDRAL". IF test evaluated as false. Skipping command CHARMM> Crystal define octa @7 @8 @9 @theta @theta @theta Parameter: 7 -> "67.3651" Parameter: 8 -> "67.3651" Parameter: 9 -> "67.3651" Parameter: THETA -> "109.4712206344907" Parameter: THETA -> "109.4712206344907" Parameter: THETA -> "109.4712206344907" Crystal Parameters : Crystal Type = OCTA A = 67.36510 B = 67.36510 C = 67.36510 Alpha = 109.47122 Beta = 109.47122 Gamma = 109.47122 CHARMM> open read card unit 1 name "rhomba.xtl" VOPEN> Attempting to open::rhomba.xtl:: OPNLGU> Unit 1 opened for READONLY access to rhomba.xtl CHARMM> crystal read card unit 1 CRYSTAL FILE BEING READ FROM UNIT 1 TITLE> * FILE: DODECAHEDRON.XTL TITLE> * CRYSTAL DEFINE RHOMBOHEDRAL A=B=C THETA=109.4712175881765 TITLE> * COMMONLY CALLED TRUNCATED DODECAHEDRON TITLE> * DATE: 11/22/96 7:57:32 CREATED BY USER: ROUXB TITLE> * TITLE> * FILE: DODECAHEDRON.XTL TITLE> * CRYSTAL DEFINE RHOMBOHEDRAL A=B=C THETA=109.4712175881765 TITLE> * COMMONLY CALLED TRUNCATED DODECAHEDRON TITLE> * DATE: 11/22/96 7:57:32 CREATED BY USER: ROUXB TITLE> * THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET 14 Transformations have been processed. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> label donextl CHARMM> CHARMM> image byseg xcen 0.0 ycen 0.0 zcen 0.0 select .not. resname tip3 end SELRPN> 906 atoms have been selected out of 14316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> image byres xcen 0.0 ycen 0.0 zcen 0.0 select resname tip3 end SELRPN> 13410 atoms have been selected out of 14316 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> CHARMM> ! turn on faster options and set-up SHAKE CHARMM> faster on MISCOM> FAST option ON. Scalar FAST Mode CHARMM> CHARMM> cons fix select .not. resn tip3 end SELRPN> 906 atoms have been selected out of 14316 CHARMM> CHARMM> minimize conj nstep 30 tolenr 1.00 nprint 10 - CHARMM> cutnb 10.0 rdie eps 2.0 vswitch shift bycb SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 876 292 292 0.00 2 C002 has 267 89 89 0.00 3 C003 has 261 87 87 0.00 4 C004 has 855 285 285 0.00 5 C005 has 228 76 76 0.00 6 C006 has 768 256 256 0.00 7 C007 has 786 262 262 0.00 Total of18357 atoms and 6076 groups and 5878 residues were included NONBOND OPTION FLAGS: ELEC VDW ATOMs RDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 10.000 CTEXNB =999.000 CTONNB = 6.000 CTOFNB = 8.000 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 15987 exclusions and 2396 interactions(1-4) found 746 group exclusions. found 0 image 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 9 9 9 10.00000000000000 Using Image CUBE search 9 9 9 10.00000000000000 NBNDGCM found: 2219447 atom pairs 415 image atom pairs CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 30 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 1.0000000 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 -19472.16962 0.00000 7.81252 0.00000 MINI INTERN> 0.00017 0.00002 0.00000 0.00000 0.00000 MINI EXTERN> 4922.46291 -24394.63273 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -23737.14160 4264.97198 1.91801 2.36396 MINI INTERN> 360.27885 147.83093 0.00000 0.00000 0.00000 MINI EXTERN> 3068.44942 -27313.70080 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -24715.21120 978.06959 1.29167 2.50654 MINI INTERN> 573.85574 252.14862 0.00000 0.00000 0.00000 MINI EXTERN> 2963.02891 -28504.24447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -25266.42730 551.21610 1.19385 2.00490 MINI INTERN> 587.84097 227.12188 0.00000 0.00000 0.00000 MINI EXTERN> 3362.92469 -29444.31484 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 30) exceeded. 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> 30 -25266.42730 551.21610 1.19385 0.02000 CONJ INTERN> 587.84097 227.12188 0.00000 0.00000 0.00000 CONJ EXTERN> 3362.92469 -29444.31484 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> cons fix select none end SELRPN> 0 atoms have been selected out of 14316 CHARMM> cons harm force 30.0 select .not. resn tip3 end SELRPN> 906 atoms have been selected out of 14316 CSTRAN: Harmonic Restraints ABSOlute type as set number 1. Number of selected atoms: 906 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 906 atoms are restrained. CHARMM> minimize conj nstep 30 tolenr 1.00 nprint 10 - CHARMM> cutnb 10.0 rdie eps 2.0 vswitch shift bycb SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 870 290 290 0.00 2 C002 has 264 88 88 0.00 3 C003 has 252 84 84 0.00 4 C004 has 858 286 286 0.00 5 C005 has 231 77 77 0.00 6 C006 has 774 258 258 0.00 7 C007 has 795 265 265 0.00 Total of18360 atoms and 6077 groups and 5879 residues were included found 0 image group exclusions. NONBOND OPTION FLAGS: ELEC VDW ATOMs RDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 10.000 CTEXNB =999.000 CTONNB = 6.000 CTOFNB = 8.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 2.000 NBXMOD = 5 There are 2219447 atom pairs and 18383 atom exclusions. There are 0 group pairs and 746 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 2885281 ATOM PAIRS AND 0 GROUP PAIRS == IMAGES === SPACE FOR 539 ATOM PAIRS AND 0 GROUP PAIRS Using Image CUBE search 9 9 9 10.00000000000000 NBNDGCM found: 2314983 atom pairs 427 image atom pairs CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 30 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 1.0000000 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 -25372.11106 105.68377 1.18087 0.00000 MINI INTERN> 610.40999 323.99836 6.37058 264.21705 3.00835 MINI EXTERN> 3149.53097 -29729.64636 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -25665.67757 293.56650 1.08902 1.05264 MINI INTERN> 580.40819 296.81402 8.10328 265.35393 4.89646 MINI EXTERN> 3131.78560 -29960.76732 0.00000 0.00000 0.00000 MINI CONSTR> 7.72828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -25874.64845 208.97088 0.84086 1.04292 MINI INTERN> 569.89908 290.93137 7.67483 267.06393 3.56130 MINI EXTERN> 3307.67443 -30328.98193 0.00000 0.00000 0.00000 MINI CONSTR> 7.52854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -26101.23698 226.58853 0.95758 1.29924 MINI INTERN> 597.17981 293.24375 7.32406 265.06996 4.24152 MINI EXTERN> 3697.88132 -30975.93256 0.00000 0.00000 0.00000 MINI CONSTR> 9.75517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 30) exceeded. 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> 30 -26101.23698 226.58853 0.95758 0.02000 CONJ INTERN> 597.17981 293.24375 7.32406 265.06996 4.24152 CONJ EXTERN> 3697.88132 -30975.93256 0.00000 0.00000 0.00000 CONJ CONSTR> 9.75517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> shake bonh tol 1.0e-8 para SHKCOM> SHAKE parameters: TOL = 0.1000D-07 MXITer = 500 13852 constraints will held by SHAKE. CSHKINI: Fast shake initialized with 442 bond contraints and 4470 water constraints (3-center). CHARMM> CHARMM> set begin 1 Parameter: BEGIN <- "1" CHARMM> set end 5 Parameter: END <- "5" CHARMM> set current @begin Parameter: BEGIN -> "1" Parameter: CURRENT <- "1" CHARMM> set status start Parameter: STATUS <- "START" CHARMM> CHARMM> ! Set-up directories for dynamics output CHARMM> system "mkdir kun res crd coor size" Invoking: mkdir kun res crd coor size CHARMM> CHARMM> ! Harmonically restrain the backbone to permit the solvent to become CHARMM> ! "equilibrated" to the solute. CHARMM> cons harm clear CHARMM> cons harm force 5.0 mass select - CHARMM> ( type c .or. type o .or. type ca .or. type n ) end SELRPN> 243 atoms have been selected out of 14316 CSTRAN: Harmonic Restraints ABSOlute type as set number 1. Number of selected atoms: 243 Reference coordinates set to main coordinates. Mass weighting will be used for new restraints. The force constant of 5.00000 will be used. An exponent of 2 will be used. The XYZ scale factors are: 1.00000 1.00000 1.00000 A total of 243 atoms are restrained. CHARMM> CHARMM> label dodyn CHARMM> CHARMM> title RDTITL> * INITIAL DYNAMICS FOR 1FSC. RDTITL> * DYNAMICS INITIATED FROM COOLED STRUCTURE AND HEATED TO 298K OVER RDTITL> * 50K STEPS (100PS) OF DYNAMICS. PRODUCTION FOR 1 20PS WINDOW. RDTITL> * HARMONIC FORCE RESTRAINTS APPLIED DURING THE FIRST 20PS USING A FORCE RDTITL> * CONSTANT OF 5*MASS. RDTITL> * CHARMM> CHARMM> if current gt @begin goto newres Parameter: BEGIN -> "1" Comparing "1" and "1". IF test evaluated as false. Skipping command CHARMM> goto skip CHARMM> open unit 3 write form name "res/@PDBFILE_e@CURRENT.res" Parameter: PDBFILE -> "1FSC" Parameter: CURRENT -> "1" VOPEN> Attempting to open::res/1fsc_e1.res:: OPNLGU> Unit 3 opened for WRITE access to res/1fsc_e1.res CHARMM> open unit 20 write form name "kun/@PDBFILE_e@CURRENT.kun" Parameter: PDBFILE -> "1FSC" Parameter: CURRENT -> "1" VOPEN> Attempting to open::kun/1fsc_e1.kun:: OPNLGU> Unit 20 opened for WRITE access to kun/1fsc_e1.kun CHARMM> CHARMM> prnlev 4 CHARMM> ! Run dynamics in periodic box CHARMM> dynamics cpt leap @status timestep 0.002 nstep 10000 nprint 10 iprfrq 1000 - CHARMM> firstt 298 finalt 298 twindl -5.0 twindh 5.0 - CHARMM> ichecw 1 teminc 30.0 ihtfrq 20 ieqfrq 200 - CHARMM> iasors 1 iasvel 1 iscvel 0 isvfrq 1000 - CHARMM> iunwri 3 nsavc 0 nsavv 0 iunvel 0 - CHARMM> iunread 4 iuncrd 0 kunit 20 - !{* Nonbond options *} CHARMM> inbfrq -1 imgfrq -1 ilbfrq 0 bycb - !use bycube image nonbond list generator CHARMM> eps 1.0 cutnb @cutoff cutim @cutoff ctofnb @ctofnb ctonnb @ctonnb vswi - CHARMM> rq 1000 - CHARMM> firstt 298 finalt 298 twindl -5.0 twindh 5.0 - CHARMM> ichecw 1 teminc 30.0 ihtfrq 20 ieqfrq 200 - CHARMM> iasors 1 iasvel 1 iscvel 0 isvfrq 1000 - CHARMM> iunwri 3 nsavc 0 nsavv 0 iunvel 0 - CHARMM> iunread 4 iuncrd 0 kunit 20 - !{* Nonbond options *} CHARMM> inbfrq -1 imgfrq -1 ilbfrq 0 bycb - !use bycube image nonbond list generator CHARMM> eps 1.0 cutnb @cutoff cutim @cutoff ctofnb @ctofnb ctonnb @ctonnb vswi - CHARMM>