Dear all,
I'm performing PCA on a 20 nanosecond simulation of a
~200 aa protein. I performed PCA initially using only alpha carbons. I
then reperformed it by using the backbone for fitting, and the whole
protein for covar analysis.
This worked but when I looked at some of the motions using the -extr option in
g_anaeig, the side chains look strange/distorted.
I've
noticed that most reported PCA uses just alpha carbons or backbone
atoms. Does this mean that PCA is not well suited for all-atom analysis
due to fast side chain motions? Or did I make some mistake (like not
selecting the same set of atoms for fitting and analysis)? Can someone
point me toward a paper where PCA included side chains?
Thanks.
Patrick
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