[AMBER] How to analyse the PCA results?

From: Markowska <markowska.kar.gmail.com>
Date: Wed, 18 Jul 2018 18:01:59 +0200

Dear Amber users,

I would like to perform a PCA analysis of a protein's trajectories.
Something similar to this work:

I went through the cpptraj PCA tutorial,
http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/ and obtained the
diagonal matrix file and the projection trajectories.

I would also like to present my results similarily as it was shown at
Figure 2: https://www.nature.com/articles/srep07906/figures/2

How to convert the cpu-gpu-evecs.dat diagonal matrix into a file that could
be used by gnuplot to plot something similar to Figure 2?

And if I finally get the "distribution of components" plot, how would I
know, which conformation is represented by which part of the plot?

Thanks for your help!
Karolina MitusiƄska
PhD student
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Received on Wed Jul 18 2018 - 09:30:01 PDT
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