[gmx-users] a query

Anik Sen aniksen at csmcri.org
Tue Jan 24 10:58:26 CET 2012

Thanx Mark.
                   I understand that I have to change the residue names. But how to generate them. Is there any software by which I can generate or any sequence by which I may change them..

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: Tuesday, January 24, 2012 3:19 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] a query

On 24/01/2012 8:32 PM, Anik Sen wrote:
Hello Anik here.

I think its a silly question but, could not stop to ask as its between me and my gromacs job.
I am using gromacs 4.5.5. I want to run a dynamics run with DNA. I made a pdb file from vmd software. But the residue file its showing is "MOL". There is no residue type named mol. So what will be the residue files for DNA. Please suggest.

Your input to pdb2gmx needs to use residue names that match the .rtp file for your force field. Either generate it with them, or edit them in afterwards.

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