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

[Francesco Oteri]

Dear bharat,
you can try Phosfinder (http://phosfinder.bio.uniroma2.it). It is a 
website that predict phosphate binding site on protein stucture.

The paper url is:http://www.ncbi.nlm.nih.gov/pubmed/21622655


Il 31/05/2011 02:06, bharat gupta ha scritto:
> thanks ...
>
> On Mon, May 30, 2011 at 5:03 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     bharat gupta wrote:
>
>         Well, mine is a beta-barrel protein called Green Fluorescent
>         Protein. In such a case the movement of ion is very important.
>         As the ion in side the barrel can quench the fluorescence.
>         That's what I want to track..
>
>
>     You can probably address this with the methods I've described.
>      That's likely all that anyone can offer.  Spend some time looking
>     through the literature at the many kinds of systems that have been
>     addressed using SMD and/or umbrella sampling and come up with a
>     coherent plan to address your system based on what you find.
>
>
>     -Justin
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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> -- 
> Bharat
> Ph.D. Candidate
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