[gmx-users] s-s bond recognition
mahdiuni at gmail.com
Sun Nov 23 15:38:23 CET 2014
Thanks Abhishek, I will do it.
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<div>-------- Original message --------</div><div>From: Abhi Acharya <abhi117acharya at gmail.com> </div><div>Date:23/11/2014 6:03 PM (GMT+03:30) </div><div>To: Discussion list for GROMACS users <gmx-users at gromacs.org> </div><div>Cc: </div><div>Subject: Re: [gmx-users] s-s bond recognition </div><div>
I would suggest you to first try energy minimization on the protein alone
and see whether it solves the issue. If not, then try MD (without any S-S
bonds) with distance restraints on the sulfur atoms of the particular Cys
See if that resolves the issue.
On Sun, Nov 23, 2014 at 6:56 PM, Hamid Mahdiuni <mahdiuni at gmail.com> wrote:
> Hi everyone
> I’m going to run -pdb2gmx on my protein with PDB code of 2O6X. This protein
> has three S-S bonds within its crystal structure, but, after running of
> -pdb2gmx, only 2 of them recognized as S-S bond. I think that the distance
> between S atom of Cys253 and its counterpart of Cys302 is too long to form
> S-S bond. What can I do? Can I force these residues to form S-S bond in
> .gro file?
> Thanks in Advance
> Hamid Mahdiuni
> Dept. of Biology, Faculty of Science
> Razi University
> P.O.Box 6714967346
> Tel: +98 831 4274545
> Fax: +98 831 4274545
> E-mail : mahdiuni at ibb.ut.ac.ir
> mahdiuni at gmail.com
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