From: Jeff Comer (
Date: Tue Apr 12 2016 - 08:56:29 CDT

Yes, it's possible to use psfgen with multiple topologies.

I also use Packmol to make systems; however, I usually do it differently.
If you start with a psf and pdb for each component in your Packmol script,
you don't actually need to use topology files at all. Suppose that you use
Packmol to assemble a system of 215 identical molecules. You can generate a
psf for these 215 molecules using the code below. Then you can load this
psf and your packmol pdb together. The code below can be easily extended to
multiple molecules. Note that you have to put the molecules together in the
same order as in the Packmol script so that the positions in the
Packmol-generated pdb correspond to the atoms in the psf generated by the


set psf mol.psf
set pdb mol.pdb
set num 215
set segPrefix M
set outName mol_n${num}
set packMolPdb pack_mol.pdb

package require psfgen

mol new $psf
mol addfile $pdb waitfor all
set all [atomselect top all]

for {set i 0} {$i < $num} {incr i} {
    $all set segname ${segPrefix}${i}
    $all writepsf tmp.psf
    $all moveby {6 0 0}
    $all writepdb tmp.pdb

    # Load the topology and coordinates.
    readpsf tmp.psf
    coordpdb tmp.pdb

# Write the combination.
writepsf $outName.psf
writepdb $outName.pdb

# Rewrite the Packmol pdb to be consistent with the psf.
mol new $outName.psf
mol addfile $packMolPdb
set all [atomselect top all]
$all writepdb $outName.pack.pdb

Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Tue, Apr 12, 2016 at 7:33 AM, Srijita Paul <> wrote:

> hi all
> i want to create a psf file from a pdb file which contains water urea and
> protein.i have prepared the pdb from psfgen i am uploading the
> topology files top_all36_cgenff.rtf , top_all36_prot.rtf.but the following
> error is occuring-molecule destroyed by fatal eror due to unknown res name
> UREA and TIP3.but in the topology files the resnames are given UREA and
> it possible to upload multiple topology files in psfgen for
> generating a psf file?
> please give me some solution.
> thank you

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