Re: [AMBER] clustering

From: Daniel Roe <>
Date: Tue, 31 Jan 2017 12:59:59 -0500

On Tue, Jan 31, 2017 at 10:03 AM, Sowmya Indrakumar <> wrote:
> running the above commands gives me 5 representative structures. It is not very clear to me what is it taking as the reference structure. Comparing the five generated representative pdb structure to the average pdb (from the trajectory) does not give show any trend in RMSD.

The representative structure of each cluster is the frame with the
lowest cumulative "distance" (in your case RMSD) to every other frame
in the cluster. A cluster representative is just that; it's supposed
to be representative of what that cluster looks like (although this
may not always be the case). I can see how comparing representative
structures to the average structure of the cluster could be
informative ('avgout', 'avgfmt'), but it's not clear to me what
insight you can gain from comparing representatives to the overall
average structure.


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Jan 31 2017 - 10:30:03 PST
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