[gmx-users] Fwd: Simulation of protein with phosphate ion...

bharat gupta bharat.85.monu at gmail.com
Tue May 31 01:33:17 CEST 2011

Thanks for your reply..

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.

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.

On Mon, May 30, 2011 at 4:19 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> bharat gupta wrote:
>> Hi,
>> 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..
> 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.
>  I want to do the following things...
>> 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..
>> 2) After getting the site , I want to look for the binding affinities
>> between the predicted sites..
>> 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??
> 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.
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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