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.
Mark
------------------------------------------------------------------------
*From:* [email protected] [[email protected]]
on behalf of Mark Abraham [[email protected]]
*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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