[gmx-users] Re: Looking for potential phosphate binding sites

[Justin A. Lemkul]

bharat gupta wrote:
> Hi,
> 
> Is there any way to get the averaged distributions of ions around the 
> protein surface. 
> 

Start with Chapter 7 of the manual to see what's possible, then proceed to the 
relevant sections of Appendix D.  My suspicion is that the answer to your 
question is "not likely" and certainly "not directly."  You may be able to 
combine various tools (g_mdmat, g_dist, g_rdf, etc) to produce something useful.

-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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