[AMBER] PCA analysis for side chain atoms and backbone atoms

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Tue, 25 Jan 2011 20:31:03 +0100

Hi all,

I would like to make a PCA using ptraj module with ambertools - I am
not quite sure how the syntax is though.
for the backbone selection I use the following syntax


is there any easier way to select side chains?

for an analysis of the side chains will the following syntax make any sense?

strip .N,CA,C
matrix mwcovar name cc.matrix out cc.matrix
analyze matrix cc.matrix out new.matrix

Thanks in advance,

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Received on Tue Jan 25 2011 - 12:00:04 PST
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