[AMBER] clustering by attribute

From: Massimiliano Porrini <M.Porrini.ed.ac.uk>
Date: Wed, 2 Feb 2011 23:20:22 +0000

Dear Amber users,

I would like to do some cluster analysis of my long simulation
using a similarity metric different from RMSd or from DME.

As it is stated in Amber Tools manual, one can cluster by
attribute (i.e. a time series).
Specifically I would like to use the radius of gyration as

Could you please tell me which would be the syntax to use?

I have been trying with the following one, but it does not work:

trajin ../../filename.mdcrd.gz 1000 76042
radgyr gyration :1-51
cluster out filename representative pdb average pdb averagelinkage
clusters 10 gyration sieve 100 :1-51

Many thanks in advance.


Dr. Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
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Received on Wed Feb 02 2011 - 15:30:07 PST
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