VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Dec 26 2010 - 09:25:08 CST

On Sun, Dec 26, 2010 at 9:11 AM, leila karami <karami.leila1_at_gmail.com> wrote:
> Dear VMD users
>
> I have a initial pdb file containing protein, dna and water molecules.
> I need to psf file. I want to use amber03 force field to obtain psf file.
>
> is it possible?
>
> which of autopsf and psfgen is more suitable for creating of psf file?

unless you haven't noticed, autopsf is just a front end and
GUI interface to psfgen that automates common tasks
for well behaved .pdb files.

if you do something more complex, writing a custom psfgen
script is probably more adequate.

in both cases, psfgen is going to do the job, so your question
would have to be: is my pdb file suitable for processing with
autopsf instead of psfgen directly?

only you can answer that.

in any case, you first need to find a topology
and parameter file that has the desired force
field in charmm format. to the best of my knowledge,
VMD only ships with the cornell (94) version.

axel.

> any help will highly appreciated.
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.