[AMBER] query on principal component analysis trajectory

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Sat, 12 Jun 2021 12:23:33 +0530

Dear all,

We are working on 2 protein-nucleic acid systems. The number of residues in
the protein is the same in either of the systems. The nucleic acids have
different numbers of residues- one has 20 and the other has 16. We are
trying to figure out how the removal of these 4 bases affect the protein
> If we would like to compare these using a pca, should we stick to
independent pc analysis or a combined trajectory analysis?
> when we fit the rms in the combined trajectory analysis, how could we
include the residues as the number is not uniform?
> If we include only the protein in the rms fit and find the principal
components of the protein backbone (Stripping off the nucleic acid
residues), even the trajectory would contain only the protein. But we
wanted to visualize the motion of the principal components of protein with
respect to the nucleic acid. Is there a way to include the nucleic acids in
the trajectory? I tried and failed since the evecs.dat file exclusively
contained only CA atoms and got the coordinate mismatch error when I tried
to include the nucleic acid backbone atoms.

Sruthi Sudhakar
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Received on Sat Jun 12 2021 - 00:00:02 PDT
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