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

[anu chandra]

Dear Justin,

Thanks for your immediate reply.

Is it possible to do clustering based on side-chain RMSF in gromacs?

What about dihedral angle order parameters in gromacs?. Does it provide any
information about what I want to know?

Thanking you once again

regards
Anu


On Mon, Apr 1, 2013 at 8:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
>
> --
>
> ========================================
>
> 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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