Re: seperate files-par, top and pdb files for solvents, needed?

From: Jeffrey J. Potoff (
Date: Fri Aug 17 2007 - 08:20:28 CDT

On Fri, 17 Aug 2007, jestin mandumpal wrote:

> Friends,
> I am quite new to NAMD and systems that I investigate
> are
> In order to solvate the molecule, Should I prepare
> seperate pdb, parameter and toplogy files for the
> solvent, in my case Water?

Hi Jestin,
         There are many different ways to do what you want. I have
students that like to call multiple topology files when building the system,
and others that like to put everything in a single file. Either way will
work fine. I do put each molecule in it's own PDB file, with is fairly easy
to do with "grep" if they are all in the same file. I like to have
everything in the same topology and parameter file, but have created my own,
since we use the TraPPE force field for many of our calculations instead
of Charmm.

I use Packmol to generate the initial configuration, and run a short
tcl script generate the PSF file.


Jeffrey J. Potoff
Associate Professor Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr Phone:(313)577-9357
Detroit, MI 48202 Fax: (313)578-5815

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