Dear Amber users,
I am performing PCA calculations using cpptraj in ambertools 14.
There are 630 C-alpha atoms in my protein and the mass-weighted covariance
matrix is 1890 x 1890.
I extracted the eigenvalues and the first 5 are given below.
1 0.48444
2 0.58309
3 1.08605
4 1.58621
5 1.98272
I want to calculate the percentage of variance for each eigenvector.
According to the suggestions given in the mailing list, I understand that
these are frequencies and should be converted to eigenvalues for
calculating variance.
I tried to convert them using the conversion formula,
Freq = 108.587 * sqrt( 0.6 / Eigenvalue )
(
http://archive.ambermd.org/201307/0678.html)
But, the first frequency gave a very small eigenvalue (in the range of e-06)
Am I proceeding in the right direction?
I need your valuable suggestions in calculating the percentage variance of
each eigenvector.
Thanks in advance..
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 25 2015 - 08:00:03 PST
