From: John Stone (
Date: Thu Apr 01 2004 - 11:08:11 CST

  You can't really merge them properly without using psfgen.
Li should save the aligned coordinate files first using one of the
methods I suggested. Here's a simple psfgen script that should merge
a bunch of PDB files together, probably needs a bit of cooking for real
use, but you get the idea:

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
writepsf mergedpdb.psf
writepdb mergedpdb.pdb

On Thu, Apr 01, 2004 at 03:48:21PM +0200, Gadi Oron wrote:
> Hi,
> VMD cannot (AFAIK) save merge 2 proteins. To achieve it you must save
> one of the aligned molecules and then merge bothe using psfgen.
> On Thu, 2004-04-01 at 05:42, li wrote:
> > Hi,all:
> > A very simple question.I need align two molecules in VMD, then save the two molecule coordinates in another PDB file ,but failed in finding out this command in the VMD manual.
> > thank in advance
> > --
> > USTC Alumni Email System
> --
> ================= Gadi ORON, PhD -o- Proteologics ======================
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