[gmx-users] Analysis of Protein Complex

[Saba Ferdous]

Dear Sir,

I am studying a protein complex. I have perforemed 10ns simulations. I
saved snapshots every10ps. sp all snap shopts I got were 1000.

Now I want to analyse them with respect to interactions. I want to check
the binding surfaces and binding points which come closer and incontact
during simulations. Can you devise me a way to perform such kind of
analysis. Further more I am interested to know the binding energies as
well. What sort of other analysis can be done on this complex.

-- 
Saba Ferdous
Research Scholar (M. Phil)
National Center for Bioinformatics
Quaid-e-Azam University, Islamabad
Pakistan
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