[AMBER] Principal COORDINATES analysis

From: Massimiliano Porrini <M.Porrini.ed.ac.uk>
Date: Wed, 23 Feb 2011 12:33:00 +0000

Dear all,

I would like to perform a principal coordinates (not components) analysis,
using as similarity matrix the RMSD pairwise distances.

Is there any procedure I could use within Amber software?

I know that the clusters analysis produces the above RMSD distances
matrix in a file called PairwiseDistances, but it is not in ascii format.

If there is no procedure to accomplish the principal coordinates analysis
I might diagonalize this matrix to find eigenvectors/eigenvalues and then
project the configurations onto the space of the first two eigenvectors.

But, in this case, I need to know the format of this PairwiseDistances
file in order
to use it as a input.

Any hint would be truly appreciated.

Best regards,

Dr Massimiliano Porrini
P. E. Barran Research Group
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 23 2011 - 05:00:03 PST
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