AMBER: clustering

From: julien <>
Date: Thu, 22 Sep 2005 14:10:00 +0200

Dear all,

I wish to make clustering.
I saw in the section tutorial in particular in the tutorial 4 ( Peptide Folding
- Folding TRPCage) of the PSC 2005 Workshops tutorials the presence of

my question is as follows: I don't understand the parameter radius in the
following order

kclust -mode rmsd -centroid -cdist -heavy -lsqfit \
 -radius 6 -maxerr 1 -iterate \
  ../clustfils > ../Centroid_6

which is the definition of this parameter?
it has relationship with the radius of gyration
where can I find information?

thanks for advance

sincerely yours


Julien Pecher
Laboratoire de Biophysique, DMAG, INERIS-EA 3901
Faculte de Pharmacie, 1 rue des Louvels
80037 Amiens Cedex 1, France
Tel: +33 (0)3 2282-7498 Fax: +33 (0)3 2282-7469
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Received on Thu Sep 22 2005 - 13:53:00 PDT
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