Dear all,
I'm trying to do clustering of an RNA trajectory using ptraj from amber11. This is what I do:
ptraj TSL_400ns.vac.top < ptraj.in
where ptraj.in is:
trajin ../../TSL_400ns.dry.trj 1 400000 20
cluster out clusterTSL.10 representative pdb \
average pdb averagelinkage clusters 10 rms :2-20
- with the first line I was trying to use 1 frame every 20 for the clustering. Given that I have 400,000, that'd be 20,000 frames.
- with the third line I'm trying to create 10 clusters, generated only considering residues 2 to 20.
what I get is 10 clusters in which, 19,991 frames are in the first cluster (c0), and the rest of the clusters have only one point in them.
This is not possible, I've done clustering of this RNA before using diff settings (e.g., collecting 1 frame every 100 instead of every 20) and I get clusters with nicely distributed occurences.
what do you think I have done wrong? Maybe 10 clusters is too much, maybe collecting 1 every 20 is not a good idea? We are talking about a trajectory of 400 ns here.
Thanks very much for any ideas,
Amparo
Amparo Garcia-Lopez, Ph.D.
Pharmaceutical Biochemistry
School of Pharmaceutical Sciences
University of Geneva
Quai Ernest-Ansermet 30
1211 Genève 4 - Switzerland
Tel: +41 (0)22 379 3376
Fax: +41 (0)22 379 3360
e-mail: Amparo.GarciaLopez.unige.ch
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Received on Mon Apr 15 2013 - 06:00:04 PDT
