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

Justin A. Lemkul jalemkul at vt.edu
Tue May 31 01:48:15 CEST 2011

bharat gupta wrote:
> 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. 

It sounds like steered MD and umbrella sampling would be useful.  You can pull a 
phosphate ion through the channel if that's of interest.  Otherwise, you can 
pull the phosphates from whatever binding sites you've determined to get free 
energy changes for any of these processes.



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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