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

Justin A. Lemkul jalemkul at vt.edu
Tue May 31 01:19:35 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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