On 4/2/13 4:58 AM, anu chandra wrote:
Dear Justin,
Thanks for your immediate reply.
Is it possible to do clustering based on side-chain RMSF in gromacs?
Not that I'm aware of.
What about dihedral angle order parameters in gromacs?. Does it provide any
information about what I want to know?
You can probably get some useful information, but I don't know how to calculate
such quantities in Gromacs, and any clustering you would do would have to be
external to Gromacs.
-Justin
Thanking you once again
regards
Anu
On Mon, Apr 1, 2013 at 8:28 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On Mon, Apr 1, 2013 at 4:52 AM, anu chandra <anu80...@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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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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