<div>Thanks for your reply..</div><div><br></div>Actually I came across a paper "Molecular Modeling of the RNA binding N-terminal Part of Cowpea Chlorotic Mottle Virus coat Protein in Solution with Phosphate ion"... This paper was published in 1996, by Dr. David van der Spoel.. In this paper , they were trying to find out where exactly the phosphate ions bind to the peptide. <div>
<br></div><div>I thought may be I can try this but in their case it was a peptide and I am dealing with a barrel protein. As u said that I can go for docking and binding site prediction tools.. Since I am having some of docked complexes of my protein with phosphate ion, can I use MD for checking how strong the binding is or does the ion tries to move inside the barrel. <br>
<br><div class="gmail_quote">On Mon, May 30, 2011 at 4:19 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi,<br>
<br>
I want to dock a barrel protein with phosphate ion , to look for the sites where Phosphate ion binds... I searched the gmx list but I didn't find much related threads..<br>
</blockquote>
<br></div>
You usually won't find instructions specifically tailored for your specialty application. This list is for general Gromacs usage. Occasionally you'll find a how-to for something, but that's a rare find.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I want to do the following things...<br>
1) Simulate the binding of phosphate ion with a barrel protein. Here I do not know where does the ions binds and thats what I want to find through simulation..<br>
2) After getting the site , I want to look for the binding affinities between the predicted sites..<br>
<br>
I want to know how shall I approach this.. since I don't know how many ions I have to simulate with the protein..Can anybody help or refer to some paper??<br>
<br>
</blockquote>
<br></div>
It sounds like you need to be looking at docking and/or binding site prediction algorithms, neither of which can be done with Gromacs. Running MD and hoping your PO4 stick somewhere is a great way to waste time and probably not learn anything :) There are several ways to calculate binding free energies after you've determined plausible binding sites.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</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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