AMBER Archive (2005)

Subject: AMBER: Cluster analysis by MMTSB or ptraj

From: Shuting Wei (gtg549i_at_mail.gatech.edu)
Date: Fri Oct 28 2005 - 10:30:49 CDT

Dear Amber,

I want to study the complexation between two kinds of molecules. By
simulation annealing, i created 1000 snapshots of the complex. Now i need
to do cluster analysis for that, i tried MMTSB, but it doesn't work, no
cluster was found. Anyone know how to use MMTSB for the complex study?

I also heard that we can do cluster analysis by ptraj. Anyone has idea
about how to do that?

Thanks a lot!

Shuting

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