Dear Amber users,
Since I did not receive any answer, I do not know if my email has reached you.
Hereby I forward it to you again, hopefully you have a hint to suggest me.
Cheers,
MP
---------- Forwarded message ----------
From: Massimiliano Porrini <M.Porrini.ed.ac.uk>
Date: 2011/2/2
Subject: clustering by attribute
To: AMBER Mailing List <amber.ambermd.org>
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
attribute.
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.
Regards,
MP
--
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
mozz76.gmail.com
maxp.iesl.forth.gr
--
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
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Mon Feb 07 2011 - 08:00:05 PST
