Hi Kat
You can take a look at
"New insights into the meaning and usefulness of principal component
analysis of concatenated trajectories"doi:10.1002/jcc.23811Authors
Gustavo Pierdominici-Sottile,, Juliana Palma
and
On the analysis and comparison of conformer-specific essential dynamics
upon ligand binding to a protein Grosso, M.; Kalstein, A.; Parisi, G.;
Roitberg, A. E.; Fernandez-Alberti, S. J. Chem. Phys. 142, 245101. (2015)
Cheers
adrian
On 6/24/16 2:38 PM, Kat G wrote:
> 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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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Jun 24 2016 - 12:00:03 PDT
