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

Justin A. Lemkul Thu, 17 Feb 2011 17:45:42 -0800


bharat gupta wrote:

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

This list and its users should not supplant your own literature searching andlearning experience. A simple Google search for:


"molecular dynamics" "metal binding"

yields over 60,000 results. Doubtless some of these will be useful in gettingyou started. There are, of course, more sophisticated literature searchingtools that might serve you even better.


-Justin

On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman <ran.fried...@lnu.se<mailto:ran.fried...@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.m...@gmail.com
<mailto: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
<mailto:gmx-users@gromacs.org>>
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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 <mailto:monu46...@yahoo.com>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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