[AMBER] PCA multiple trajectories for mutants and wild type

From: Stejskal, Lenka <lenka.stejskal.15.ucl.ac.uk>
Date: Wed, 11 Jul 2018 11:48:26 +0000

Dear Amber users,

I am trying to compare multiple trajectories of either wild type and a few mutant of the protein to compare differences in their dynamics. I have several ideas how to do this and any experience/ideas would be appreciated.

I create the matrix based on all trajectories and project the 1st and 2nd PC onto individual trajectories to see a difference in the occupied phase space. Alternatively, as I am trying to compare the mutants to the wild type, I could create the matrix based just on the wild type and project trajectories of the mutants on these eigenvectors. I believe this might be a better measure.

I am however making an assumption that the motion is comparable. Could this be an issue? Is there any way I can confirm this?

I will also calculate the eigenvectors for each trajectory individually. Is there a way to compare how similar these are?

Thank you very much for your help!

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Received on Wed Jul 11 2018 - 05:00:02 PDT
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