Hi,
I believe the manual has an error and that the attribute functionality
of clustering is not yet fully implemented. The manual states: "It is
now also possible to cluster by attribute...will be discussed later",
but it is never referenced again. Currently you have to use either rms
or dme as your distance metric (ptraj cluster experts - please correct
me if I'm missing something here).
Also, unlike the distance, angle, dihedral etc. commands the 'radgyr'
command does not as of yet process a 'name' argument (and therefore
does not go on the scalarStack) so unfortunately you would not be able
to use radius of gyration to cluster anyway.
-Dan
On Wed, Feb 2, 2011 at 6:20 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk> wrote:
> 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
>
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Received on Mon Feb 07 2011 - 09:30:15 PST
