AMBER: Clustering - MMTSB Toolkit kclust

From: <>
Date: Wed, 07 Dec 2005 13:43:52 -0500

Hi Amber Community,
        Following one of the tutorials (Tutorial 8 - I learned of the clustering script kclust that comes with
the MMTSB toolkit that can be used to analyze Amber MD.crd files. My
question is on the use of the radius term that is specified for
clustering. The command looks like:

kclust -mode rmsd -centroid -cdist -heavy -lsqfit -radius 3 -maxerr 1
-iterate ../clustfils > ../Centroid_3

The MMTSB documentation for clustering mentions the use of the radius
term, but it does not explain how it used. Does anyone have a paper
that explains clustering, or could briefly explain how the radius
term is used in determining clusters.

Many Thanks,
Karl N. Kirschner, Ph.D.
Visiting Assistant Professor of Chemistry
Hamilton College, Clinton NY 13323

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Received on Wed Dec 07 2005 - 18:53:00 PST
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