[gmx-users] RE: simulation of a metal binding sites

[bharat gupta]

Thankx for the reply ...

Can you refer some papers which can be helpful for me to do MD simulation of
proteins with ions ... It will be of great help.. I searched the gromacs
user list but couldn't get much material..

On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman <ran.friedman at lnu.se> wrote:

> Hi,
>
> There are methodological difficulties in simulating multivalent ions
> together with proteins. Check the mailing list for a discussion and
> reference. This is not an
> issue of Gromacs but of dealing with protein-ion interactions using a
> classical non-polarisable force field. Check the literature.
>
> Ran.
>
> Message: 3
> Date: Wed, 16 Feb 2011 20:14:07 -0800
> From: bharat gupta <bharat.85.monu at gmail.com>
> Subject: [gmx-users] RE: simulation of a metal binding sites
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <AANLkTin06UT6+WrFpZ4A79fQ9G-GALMk35UxeCPH+hCe at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I have incorporated some metal binding sites(zinc ion) in my protein. Now I
> want to see whether that region binds to zinc ions or not and what is the
> effect of ion binding to the topology of the protein .. Can this be done
> using gromacs and how ??
>
> Regards
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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