Thankx for the reply ...<div><br></div><div>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..<br>
<br><div class="gmail_quote">On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman <span dir="ltr"><<a href="mailto:ran.friedman@lnu.se">ran.friedman@lnu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi,<br>
<br>
There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an<br>
issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literature.<br>
<br>
Ran.<br>
<br>
Message: 3<br>
Date: Wed, 16 Feb 2011 20:14:07 -0800<br>
From: bharat gupta <<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>><br>
Subject: [gmx-users] RE: simulation of a metal binding sites<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
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<div><div></div><div class="h5"><br>
Hi,<br>
<br>
I have incorporated some metal binding sites(zinc ion) in my protein. Now I<br>
want to see whether that region binds to zinc ions or not and what is the<br>
effect of ion binding to the topology of the protein .. Can this be done<br>
using gromacs and how ??<br>
<br>
Regards<br>
<br>
--<br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343<br>
Mobile no. - 010-5818-3680<br>
E-mail : <a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a><br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>
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