[AMBER] 3D projection of pairwise-RMSD

From: Sangeetha B <sangeetha.bicpu.edu.in>
Date: Fri, 13 Dec 2013 19:41:57 +0530

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

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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Received on Fri Dec 13 2013 - 06:30:02 PST
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