Re: [AMBER] 3D projection of pairwise-RMSD

From: David A Case <>
Date: Fri, 13 Dec 2013 13:08:40 -0500

On Fri, Dec 13, 2013, Sangeetha B wrote:
> I have extracted a 2D RMSD matrix but it is not helpful to understand the
> conformational clustering.
> The method described by Levitt, M in 1983 (J. Mol. Biol. 168, 621-657)
> explains a method of RMSD analysis where after projection into 2D space,
> the distances between a set of points in two-dimensional plane explains the
> RMS deviations between a set of protein structures. This method can easily
> identify a transition state which is generally the first structure exiting
> the first cluster.
> I would like to generate a plot of this nature so that a transition state
> can be easily identified.

This is not in principle a very difficult calculation: you need to construct
and diagonalize the metric matrix, then reconstruct points using only the
largest two eigenvalue/eigenvector pairs. That gives you a two-dimensional
vector for each structure, which is then plotted and analyzed.

That said, I don't know of anything in Amber that does this analysis. It
might make sense to go onto Dan's (already extensive!) to-do list.


AMBER mailing list
Received on Fri Dec 13 2013 - 10:30:03 PST
Custom Search