Many thanks Daniel,
What you wrote is exactly what I had perceived.
Then, I think we are almost sure that it is not possible (yet)
to use different attributes than RMSd or DME.
Cheers,
MP
2011/2/7 Daniel Roe <daniel.r.roe.gmail.com>:
> 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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>>
>
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--
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 - 10:30:06 PST
