AMBER Archive (2004)

Subject: AMBER: Question on Clustering Analysis

From: Chen, Ya (ya.chen_at_roswellpark.org)
Date: Tue Jul 27 2004 - 13:26:30 CDT

Hi,

(I may be asking this question in the wrong place.)
I am trying NMRCLUST to do clustering analysis of Amber trajectories. I could only make it work on a small set (<1000 pdb files). The problem is, if I record every snapshot to a pdb file, eventually, I get more than 10000 models from a production run. NMRCLUST does not seem to handle that many models very well (or it's because of my computer, not sure yet.)
My question is: how do people normally do this clustering analysis or what's the generally accepted procedure/protocol?
It appears to me that it is not very practical or necessary to use NMRCLUST on all the snapshot models.
Thanks for your advise.

Chen
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