RE: Force field design

From: Abhishek TYAGI (
Date: Sat Jul 19 2014 - 07:44:53 CDT

Dear Kenno,

Thankyou for the suggestion, I had read all the information provided so far and gone through the links in detail. But still I have a silly question, right now I have a.mol2 file and I got CGenFF a.str file, and for psfgen If I use a.str file it shows error, therefore I used CHARM-GUI to get psf and pdb file, I tried doe quick md on C-GUI it gives some topology and prm file, I used them for my simulation and got error, and for other files top and prm I still confused how to proceed.

From: <> on behalf of Kenno Vanommeslaeghe <>
Sent: Thursday, July 17, 2014 1:24 AM
Subject: Re: namd-l: Force field design

On 07/15/2014 12:55 PM, Abhishek TYAGI wrote:
> 1. I tried CGenFF and got a *.str file but the data in the file is different from my input file i.e. mol2 file, the pdb format is different from the *.str file.

The str file contains a force field for your molecule, while the mol2 and
pdb formats contain a geometry. How could the data not be different???

The str file is a concatenated topology and parameter file. NAMD knows to
ignore the topology section and can read the file as it is.
I believe psfgen does the same (read the topology and ignore the
parameters) though I'm less sure about that.

> 2. I tried to get force field from swissparam website and received the different file as *.par, *.top file, I tried MD on this field it runs successful, but the question is that is this correct approach?

It is strongly encouraged to search the archive before posting a question.
If you had, you would have discovered the use of SwissParam for
condensed-phase calculations is discouraged, and found advise on better
ways to do it:

Christopher Mayne's advice in this thread is sound.

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