VMD-L Mailing List

From: Yang Yang (yang.yang_at_wmich.edu)
Date: Mon Apr 26 2004 - 21:55:45 CDT

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