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

[Justin A. Lemkul]

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

-- 
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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

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