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,
MP
--
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
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Wed Feb 23 2011 - 05:00:03 PST
