VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 03 2010 - 13:40:30 CDT

Hi,
  You want to do something more like this (cut out of another script):

proc mergeallpdbs { workdir basefilename } {
  global env

  package require psfgen
  package require readcharmmtop

  # this next line is a total hack and needs to be updated
  set topologyfile [format "%s/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp" $env(VMDDIR)]

  psfcontext new
  resetpsf
  topology $topologyfile
  pdbalias residue HIS HSD

  set nseg 1
  foreach pdb [lsort [glob $workdir/*.pdb]] {
    set segid V$nseg
    puts stdout "PDB: $pdb $segid"
    segment $segid {
      first NONE
      last NONE
      pdb $pdb
    }
    coordpdb $pdb $segid
    incr nseg
  }

  guesscoord

  set psffilename [format "%s.psf" $basefilename]
  set pdbfilename [format "%s.pdb" $basefilename]
  writepsf $psffilename
  writepdb $pdbfilename
}

On Wed, Nov 03, 2010 at 01:30:40PM -0500, vani panguluri wrote:
> #read the files
>
> coordpdb 1k4u.pdb
>
> coorpdbd apocynin.pdb
>
> #Write the protein and membrane into one combined file
>
> writepsf apocynin_merged
>
> writepdb apocynin_merged
>
> this was the script i had used...
>
> On Wed, Nov 3, 2010 at 1:03 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> It would be helpful if you told us something about _how_ you were
> attempting to merge the structures, as you haven't specified anything
> about what script or tool you're trying to use to do this. To get any
> sort of useful feedback, you need to be completely explicit. Without
> such information, nobody can guess what you're doing, nor why it isn't
> working.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Wed, Nov 03, 2010 at 12:18:16PM -0500, vani panguluri wrote:
> > Hello,
> >
> > While i am performing merging of two files one containg 1470 with
> the file
> > containing 22 but i am unable to merge them both as in the output i
> am
> > getting only the 1468 atoms which doesn't having the information
> about the
> > file containing 22 atoms can one give me any suggestions how to
> merge
> > these two files.
> >
> > Thanks & Regards,
> > Vani
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078