Hi all,
I am using PCA to highlight concerted motions different when protein is
free and bound with many ligands. Projections of individual trajectories on
the first several PCs calculated from combined trajectories are
significantly different. Then how can I trace back to each trajectory to
see which residues in each system contribute to motions in those combined
PCs.
Could you please show me how to apply PCA and cluster analysis to
investigate changes in dynamics of protein when unbound and bound with
different ligands. In some references for the use of PCA and cluster
analysis, the purpose of those studies is to prove for convergence, rather
than analyzing the differences among trajectories. I tried to follow the
study from this paper
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300347/pdf/10388775.pdf, but
still confused of what they did and what cpptraj can calculate.
Thanks for any suggestion.
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Received on Fri Jun 24 2016 - 12:00:03 PDT
