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

[Ran Friedman]

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>
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        <AANLkTin06UT6+WrFpZ4A79fQ9G-GALMk35UxeCPH+hCe at mail.gmail.com>
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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
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Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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