Hi,
I believe the analysis you are referring to is the construction of a graph
where the vertices represent structures and the edges represent the RMSD
between the structures. To my knowledge there you can't do this exactly in
Amber, but you can calculate a 2D RMSD matrix with cpptraj or ptraj. For
example, to look at the 2D RMSD between C-alpha atoms (cpptraj):
2drms .CA out ca2drms.gnu
The ".gnu" extension tells cpptraj to write the file in gnuplot-readable
format.
Hope this helps,
-Dan
On Fri, Dec 13, 2013 at 7:11 AM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
> Dear Amber users,
>
> I am working on protein folding/unfolding problem and I came across an
> article http://www.sciencedirect.com/science/article/pii/S0022283696901722
> .
>
> I am aware of the problem in identifying a transition state in protein
> unfolding trajectory and this article (and few other related publications
> by Valerie Daggett) identify the transition state by *Ca RMSD based
> conformational clustering and its projection onto 3D space. *
>
> An analysis tool to obtain such a projection is available in CHARMM
> (RMSDyn).
>
> Is it possible to perform a similar analysis using AMBER.
>
> Any help in this regard would be grateful.
>
>
>
> --
> Thank you,
>
> With regards,
> B. Sangeetha
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
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) 585-6208 (Fax)
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Received on Fri Dec 13 2013 - 09:00:03 PST
