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

[Justin A. Lemkul]

bharat gupta wrote:
> 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..
> 

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

"molecular dynamics" "metal binding"

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

-Justin

> On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman <ran.friedman at lnu.se 
> <mailto: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
>     <mailto: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
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID:
>            <AANLkTin06UT6+WrFpZ4A79fQ9G-GALMk35UxeCPH+hCe at mail.gmail.com
>     <mailto:AANLkTin06UT6%2BWrFpZ4A79fQ9G-GALMk35UxeCPH%2BhCe 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 <mailto:monu46010 at yahoo.com>
>     -------------- next part --------------
>     An HTML attachment was scrubbed...
>     URL:
>     http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html
> 
>     --
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> 
> -- 
> 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 <mailto:monu46010 at yahoo.com>
> 

-- 
========================================

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

========================================