From: Axel Kohlmeyer (
Date: Thu Dec 02 2010 - 10:39:53 CST

hi pat,

On Thu, Dec 2, 2010 at 8:15 AM, Patrick Fleming <> wrote:
> I would like to equilibrate a phospholipid membrane other than the two
> supplied with VMD. I have a PDB file of the new lipid but it appears that I
> would have to make separate PDB files for each lipid molecule in order to
> use psfgen. It this really necessary?
> In other words, given a PDB file of many dilaurylPC molecules and the
> appropriate topology and parameter files how do I generate the psf file?

i would just create the psf for a single lipid molecule from a single molecule
pdb file and then replicate the lipid and write out the psf for that. since the
psf file has no coordinates, it doesn't matter whether the replicated system
is reasonable for as long as the bonding topology is correct.

one way to get the replicated psf would be to use the topotools plugin.

package require topotools
mol new my.psf waitfor all
mol addfile my pdb waitfor all

::TopoTools::replicatemol top 1 1 <# of lipids>

animate write psf replicated.psf


> Pat Fleming
> --
>     _o
>    ' / '-       __o
>   _|\          \<,
>   ....|......( )/( )...

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.