[AMBER] principal component analysis

From: abdennour braka <abdennour.braka.univ-orleans.fr>
Date: Mon, 11 May 2015 11:27:13 +0200

Dear Amber users,
I have sampled a protein conformations with REMD to use frames in a
multi conformational screening.
To compare the results of the MD with RX structures, I have added the RX
to the trajectory, aligned all conformations on the same reference and
performed a PCA on the heavy atoms of the active site.
However, I found that in the 3 first PC (PC1, PC2, PC3) my departure RX
structure of the MD is far from the first frame of the MD.
Do you have any idea why I find this difference and if there is another
way to compare RX conformations with MD frames.
Thank you for any replies.

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Received on Mon May 11 2015 - 02:30:03 PDT
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