Hi,
In the upcoming release of AmberTools (soon) you will be able to
cluster using multiple dihedral data sets with cpptraj.
-Dan
On Mon, Apr 1, 2013 at 1:40 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear amber users,
>
> I am working with protein-ligand interaction and using Amber 11 for
> simulation. 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 Amber?. Can any
> one suggested me a way to proceed with this sort of analysis?
>
> Waiting for your valuable reply.
>
> Thanks in advance
>
> Best regards
> Anu
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Apr 02 2013 - 08:00:03 PDT
