[gmx-users] a query

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 24 11:14:50 CET 2012

On 24/01/2012 8:58 PM, Anik Sen wrote:
> 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..

Only your text editor. Wherever you got your coordinates from either had 
the residue names and you lost them, or it never had them at all. You 
may wish to reconsider your source.


> ------------------------------------------------------------------------
> *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.
> Mark

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