Hi all,
I am trying to use PCA to study simulations of one protein in its apo form
and holo form with 3 different ligands. After doing PCA separately for each
system, the correlation is quite different among systems, compared with
what we are expecting from their binding free energy. For example, the
strongest binding activator would mostly stabilize the protein, and then
having the least number of eigenvectors to represent 90% of all possible
modes.
I suppose that it may be wrong when I made a comparison based on different
types of eigenvectors in 4 systems. I am not sure that these eigenvectors
reflect the same mode of action in 4 cases or not. How could I get the same
type of eigenvectors in both apo and holo-protein to make comparison
possibly useful.
I have heard about combined-PCA by concatenating different trajectories.
Could it be done by cpptraj.
Thanks
kat
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Received on Wed Jun 08 2016 - 18:30:02 PDT
