As long as you have a 1:1 mapping among the atoms selected for the PCA; you want to do "combined PCA" so that the modes are equivalent in each (i.e. combine trajectories and separately project on each trajectory). I think there is a tutorial on amberhub.chpc.utah.edu but that site is hanging at the moment (I alerted the team).
--tec3
________________________________________
From: Reza Khayat <rkhayat.ccny.cuny.edu>
Sent: Wednesday, January 19, 2022 2:04 PM
To: AMBER Mailing List
Subject: [AMBER] Comparing trajectories
Hi,
I have a naïve question. Is it possible to compare the conformational states that a protein complex can adopt under two different conditions? If I have a trajectory for each condition, can I do PCA for each condition and compare the PCA results? Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
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Received on Wed Jan 19 2022 - 13:30:03 PST
