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.m...@gmail.com>
Subject: [gmx-users] RE: simulation of a metal binding sites
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
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<aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@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
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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