[AMBER] PCA Contributions

From: Pavan G <pavanamber.gmail.com>
Date: Thu, 25 Jul 2013 16:20:55 -0400

Hello All,

I have a protein with 618 residues and I used ptraj to perform PC analysis
on the protein.

This code:
*rms first out rms .CA,C,N*
*image center*
*matrix mwcovar name mixedma .CA,C,N*
*analyze matrix mixedma out evecs.dat.mixed vecs 5*

gave me a 5562x5562 matrix file which also has these lines:

 5562 5562
    1 0.80680
    2 1.09819
    3 1.67464
    4 2.01560
    5 2.39907

Do the last 5 lines correspond to the 5 eigenvectors? If yes then the
contribution of
1st eigen vector in explaining the motion = 0.8068/[0.8068+1.098+...2.399]

But this would mean that contribution of 2nd eigenvector is more than 1st
eigenvector which seems incorrect since

Can someone explain what I am missing here?

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Received on Thu Jul 25 2013 - 13:30:03 PDT
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