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  5/22/ 0 at 11:21:47 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"
 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 "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: SHAPE <- "CUBIC"
  
 CHARMM>    if @?crystal eq 0 set crystal = false
 Comparing "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: CRYSTAL <- "FALSE"
  
 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 "0" and "0".
 IF test evaluated as true.  Performing command
 Parameter: SOLVATE <- "FALSE"
  
 CHARMM>    !  Read the parameter and topology files:
 CHARMM>    goto readparams
  
 CHARMM>    prnlev 0 node 0
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
  
 CHARMM>    wrnlev 2 node 0
 **** Warning ****  The following extraneous characters
 were found while command processing in MISCOM
 NODE 0
  
 CHARMM>    goto fromreadparams
  
 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 = 0}' > awk.file"
Invoking: echo 'BEGIN {write = 0}' > awk.file
  
 CHARMM>    system "echo '$1 == "TER"  {write += 1;}'>> awk.file"
Invoking: echo '$1 == "TER"  {write += 1;}'>> awk.file
  
 CHARMM>    system "echo '{' >> awk.file"
Invoking: echo '{' >> awk.file
  
 CHARMM>    system "echo 'if ($4 == "HIS") sub("HIS","HSD");' >> awk.file"
Invoking: echo 'if ($4 == "HIS") sub("HIS","HSD");' >> awk.file
  
 CHARMM>    system "echo 'if ( write == 0 ) {print $0 "@PDBFILE" ;}' >> awk.file"
 Parameter: PDBFILE -> "1FSC"
Invoking: echo 'if ( write == 0 ) {print $0 "1FSC" ;}' >> awk.file
  
 CHARMM>    system "echo '}'>> awk.file"
Invoking: echo '}'>> awk.file
  
 CHARMM>    system "echo '{if ( write == 1 ) {' >> awk.file"
Invoking: echo '{if ( write == 1 ) {' >> awk.file
  
 CHARMM>    system "echo 'if ($1 == "TER")  {print "END" ;}'>> awk.file"
Invoking: echo 'if ($1 == "TER")  {print "END" ;}'>> awk.file
  
 CHARMM>    system "echo '}}'>> awk.file"
Invoking: echo '}}'>> awk.file
  
 CHARMM>    !  Beyond column 72 we should have the segid, some NMR files don't do this.  Add
 CHARMM>    !  segid after column 72 using cut and awk.
 CHARMM>    system "cut -b 1-72 pdb_orig | awk -f awk.file > pdb_new"
Invoking: cut -b 1-72 pdb_orig | awk -f awk.file > 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 HSD 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>    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>    coor copy compare
 SELECTED COORDINATES COPIED TO THE COMPARISON SET.

  
 CHARMM>     
  
 CHARMM>    coor orie

 ORIENT THE COORDINATES TO ALIGN WITH AXIS

 MOMENTS
  53466.59103700  12915.06528957 -15448.05366951
                  33093.72386295 -16665.16403733
                                  36023.59929906

 Transpose of the rotation matrix
     0.515163   -0.455478   -0.726049
    -0.505946    0.522160   -0.686562
     0.691827    0.721033    0.038551
 CENTER OF ATOMS BEFORE TRANSLATION     3.67378    19.35494     0.93632
 AXIS OF ROTATION IS -0.704305  0.709449  0.025252  ANGLE IS   87.83

 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS.

  
 CHARMM>    coor stat
 STATISTICS FOR  906 SELECTED ATOMS:
    XMIN =  -17.642067 XMAX =   17.975566 XAVE =    0.000000
    YMIN =  -20.062431 YMAX =   11.593922 YAVE =    0.000000
    ZMIN =  -11.131808 ZMAX =   10.559502 ZAVE =    0.000000
    WMIN =    0.000000 WMAX =   69.460000 WAVE =   14.251755
  
 CHARMM>    faster on
 MISCOM> FAST option ON.
         Scalar FAST Mode
  
 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> *  PSF FOR 1FSC SEQUENCE
 RDTITL> *
  
 CHARMM>    close unit 1
 VCLOSE: Closing unit    1 with status "KEEP"
  
 CHARMM>    open unit 1 write form name @pdbfile_notmin.pdb
 Parameter: PDBFILE -> "1FSC"
 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> *  COORDINATES FOR 1FSC BEFORE MINIMIZATION
 RDTITL> *
  
 CHARMM>    close unit 1
 VCLOSE: Closing unit    1 with status "KEEP"
  
 CHARMM>    prnlev 0
  

 CHARMM>    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 CHARMM>    !          HISTIDINE distance checks
 CHARMM>    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 CHARMM>      coor mindist sele resi @hisn .and. type ND1 end -
 CHARMM>                   sele .not. resi @hisn end
 Parameter: HISN -> "6"
 Parameter: HISN -> "6"
 SELRPN>      1 atoms have been selected out of    906
 SELRPN>    889 atoms have been selected out of    906

            MINIMUM DISTANCE FOR ALL SELECTED ATOMS
   83 1FSC HSD  6    ND1 - 106 1FSC THR  7    O         2.8497
  
 CHARMM>      coor mindist sele resi @hisn .and. type NE2  end -
 CHARMM>                   sele .not. resi @hisn end
 Parameter: HISN -> "6"
 Parameter: HISN -> "6"
 SELRPN>      1 atoms have been selected out of    906
 SELRPN>    889 atoms have been selected out of    906

            MINIMUM DISTANCE FOR ALL SELECTED ATOMS
   88 1FSC HSD  6    NE2 - 583 1FSC ARG  37   HH12      1.9869
  
 CHARMM>    prnlev 0
  
 CHARMM>    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 CHARMM>    !          HISTIDINE distance checks
 CHARMM>    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 CHARMM>      coor mindist sele resi @hisn .and. type ND1 end -
 CHARMM>                   sele .not. resi @hisn end
 Parameter: HISN -> "29"
 Parameter: HISN -> "29"
 SELRPN>      1 atoms have been selected out of    906
 SELRPN>    889 atoms have been selected out of    906

            MINIMUM DISTANCE FOR ALL SELECTED ATOMS
  446 1FSC HSD  29   ND1 - 420 1FSC ARG  28   HB1       3.6827
  
 CHARMM>      coor mindist sele resi @hisn .and. type NE2  end -
 CHARMM>                   sele .not. resi @hisn end
 Parameter: HISN -> "29"
 Parameter: HISN -> "29"
 SELRPN>      1 atoms have been selected out of    906
 SELRPN>    889 atoms have been selected out of    906

            MINIMUM DISTANCE FOR ALL SELECTED ATOMS
  451 1FSC HSD  29   NE2 - 690 1FSC ASN  47   OD1       2.6855
  
 CHARMM>    prnlev 0
  

 CHARMM>    coor dist cut 3.0 sele resn HS* .and. (type NE2 .or. type ND1 ) end -
 CHARMM>                           sele .not. resn HS* end
 SELRPN>      4 atoms have been selected out of    906
 SELRPN>    872 atoms have been selected out of    906

            DISTANCES FOR SELECTED ATOMS
   83 1FSC HSD  6    ND1 - 106 1FSC THR  7    O         2.8497
   88 1FSC HSD  6    NE2 - 574 1FSC ARG  37   HG2       2.8153
   88 1FSC HSD  6    NE2 - 576 1FSC ARG  37   HD1       2.8169
   88 1FSC HSD  6    NE2 - 581 1FSC ARG  37   NH1       2.8944
   88 1FSC HSD  6    NE2 - 583 1FSC ARG  37   HH12      1.9869
  451 1FSC HSD  29   NE2 - 685 1FSC ASN  47   HA        2.9270
  451 1FSC HSD  29   NE2 - 690 1FSC ASN  47   OD1       2.6855
 TOTAL EXCLUSION COUNT =         0
 TOTAL 1-4 EXCLUSIONS  =         0
 TOTAL NON-EXCLUSIONS  =         7
  
 CHARMM>     
  
 CHARMM>    stop
$$$$$$  New timer profile $$$$$
 Total time              1.27278 Other:    0.00000

                    NORMAL TERMINATION BY NORMAL STOP
                    MAXIMUM STACK SPACE USED IS   47526
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  2
                    HEAP PRINTOUT-  HEAP SIZE  10240000
                    SPACE CURRENTLY IN USE IS         0
                    MAXIMUM SPACE USED IS         22794
                    FREE LIST
            PRINHP> ADDRESS:         1 LENGTH:  10240000 NEXT:         0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.00  SECONDS 
                         CPU TIME:     1.28  SECONDS