Dear All,
I am trying to do a PCA analysis on my simulation to compare the
conformational spread btw two sumulation. Four crystal and one NMR
structure for the same protein are already available.
I would like to do
something like the figure shown in in this aMD tutorial:
http://ambermd.org/tutorials/advanced/tutorial22/section3.htm
I am not sure ho the what energy is plotted .How it should be calculated?
For now I have done
aligning all the trajectories to the average structure and then calculate
the
projections.
-------------
matrix covar name covmat out covmat-ca.dat .CA
analyze matrix covmat out evecs-ca.dat vecs 2
projection modes evecs-ca.dat out pca12-ca beg 1 end 2 .CA
------------
Tthe two averages from each of the two simulation our different..
Can I compare the two 2D projections?
If I have xtal.pdb , how to get the 2p for that structure and overlay on
the 2D projection plot?
Thanks in advance.
Best,
Bergy
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Received on Sat Dec 13 2014 - 15:00:02 PST
