[AMBER] kclust help

From: Harmeet Kaur <meet.academia.gmail.com>
Date: Thu, 2 Jul 2015 17:30:37 +0530

Dear Amber Users,

I have used the kclust programme for clustering my trajectory (from 3
different runs of 3 different PDBs, totalling 3000 structures). When radius
is set to 5, the no. of clusters obtained is 78 (for 3000 structures). I
have used iwrap=1 in my production run. While generating the dry
trajectory, I tried using 'unwrap' but that gave me even higher no. of
clusters (close to 1000). Then I tried using 'image center familiar' and
got 78 clusters which is still large for analyses.Kindly suggest what
should be done to minimize the no. of clusters without increasing the value
of radius. I'd also be grateful if anyone can send a reference on
trajectory analysis by kclust since I want to know the maximum value that
can be set for radius during clustering.

Thanks in advance
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Received on Thu Jul 02 2015 - 05:30:02 PDT
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