[gmx-users] s-s bond recognition

[mahdiuni]

Thanks Abhishek, I will do it.


Sent from Samsung Mobile

<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>
</div>Hello.
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
residues.
See if that resolves the issue.

Regards,
Abhishek

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
> Kermanshah-Iran
> Tel:  +98 831 4274545
> Fax: +98 831 4274545
> E-mail : mahdiuni at ibb.ut.ac.ir
>             mahdiuni at gmail.com
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.