VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 17 2010 - 13:36:34 CDT

On Sun, Oct 17, 2010 at 3:26 AM, masoumeh ozmaeian <ozmaian83_at_gmail.com> wrote:
> Dear all,
> Hi,
>
> I'm trying to make a psf file of a pdb polymer chain( Nafion) and the force
> field is Charmm.

> Is it possible and how?

the answer to the first part of your question is "yes".
the answer to the second part of your question is
"it depends". in principle, there is nothing difficult
about generating a psf file, particularly for a rather
simple polymer. in practice, there are a lot of devils
hidden in the details. before going any further, a
few questions back:

what experience do you have with MD and building topologies?
do you have chamm compatible topology and parameter files?
is the pdb file for the polymer or just a monomer?
if the former, does it include water?

cheers,
    axel.

>
> Bests,
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.