VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Apr 27 2004 - 11:04:31 CDT

Hi,

Trying to build a PSF file too is overkill if you just want a PDB. If you
just want to display them together, then VMD isn't picky about the atom
numbers in the PDB file and you can just do this (in a unix shell):

  cat alanin.pdb brH.pdb | grep '^ATOM' > /tmp/cat.pdb

If you need to distinguish between the different input files, then use VMD
to set the chain, occupancy, beta, or whatever field and write out new PDB
files before pasting them together as above.

-Jim

On Mon, 26 Apr 2004, Yang Yang wrote:

> I am trying to concatenate 6 pdb files of carbonnanotubes using the
> TCL script courtesy of John Stone.
> ________________________________________________________________
> ##
> ## Load and merge all of the PDB files in a given directory
> ## Usage: source mergepdbs.txt
> ## Output is written to "mergedpdb.psf" and "mergedpdb.pdb"
> ##
>
> package require psfgen
>
> # this is a hack, just to get the topology file
> package require membrane
> set topologyfile [format "%
> s/plugins/noarch/tcl/membrane1.0/top_all27_prot_lipid.inp" $env
> (VMDDIR)]
> # topology /path/to/top_all27_prot_lipid.inp
> topology $topologyfile
> set nseg 1
> foreach pdb [lsort [glob *.pdb]] {
> set segid V$nseg
> segment $segid {
> first NONE
> last NONE
> pdb $pdb
> }
> coordpdb $pdb $segid
> incr nseg
> }
> guesscoord
> writepsf mergedpdb.psf
> writepdb mergedpdb.pdb
> -----------------------------------------------------------------
> My question is to link together these 6 pdb files of CNTs, do we
> have to provide a topology file to psfgen? If so, how to generate a
> toplogy file for CNT?
>
> I appreciate your input.
>
> Yang
>