From: Axel Kohlmeyer (
Date: Wed Aug 31 2011 - 11:34:08 CDT

On Wed, Aug 31, 2011 at 11:35 AM, Andrea Holfelder
<> wrote:
> I used the add ion plug in in vmd and was hoping that after addition of
> ions,I will be able to get both the ionized.pdb and ionized.psf
> But ionized.psf loads up in vmd and through which I could case the
> ionized.pdb file but I do not know how I can get ionized.psf file from it ?

the plugin should write out both a psf and a pdb file
_before_ loading them back into VMD. please watch
the VMD console window very carefully. depending
on what operating system you use and how you
launched VMD, those files may not be where you
expect them to be.


> Is there anyway to save the ionized.psf file as well which I will be needing
> for NAMD simulation.
> I do not want to use the psfgen to create the psf out of ionized.pdb because
> there are many residues in my pdb file also having different segid and I
> therefore can not use psfgen which would give them all the same segid and
> which then has the limit of 9999 residues in it.
> advise something please on creating psf as well pdb file easily from add
> ions plug in of vmd.

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