[gmx-users] Fwd: clustering based on side-chain conformations

[Justin Lemkul]

On Mon, Apr 1, 2013 at 4:52 AM, anu chandra <anu80125 at gmail.com> wrote:

> Dear amber users,
>
> I am working with protein-ligand interaction. The protein shows high degree
> of side-chain conformational changes and minimal backbone conformational
> changes during ligand binding. In order to capture these side chain
> flexibility, as a initial step,  I would like to do clustering based on the
> side-chain flexibility (i.e. categorise different areas in protein based on
> the degree of side chain flexibility). Is there a way to do such a
> calculation in Gromacs?. Can any one suggested me a way to proceed with
> this sort of analysis?
>
>
g_cluster does RMSD-based clustering. That's not "flexibility" per se, but
might be informative. If you do fitting based on side chains (which might
be difficult, since side chains flop around a lot), that's about as close
to achieving what you're after as I can think of using standard Gromacs
programs.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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