[AMBER] PCA: generate histogram

From: George Tzotzos <gtzotzos.me.com>
Date: Mon, 03 Aug 2015 13:46:55 +0300

I’m trying to conduct a PCA analysis of a trajectory, based on earlier suggestions from the amber list (10 March 2015).

Below is the script that I used. It seems to run as expected or almost as expected because it fails to generate the histogram as given in the last line of the input script.

I’d be grateful for any suggestions dealing with this problem.



parm 3n7h_de3_solv.prmtop
trajin prod_0-20ns.nc
rms first
average avg.nc
createcrd CRD1
reference avg.nc [ref1]
crdaction CRD1 rms @CA ref [ref1]
crdaction CRD1 matrix covar name matrixdat @CA out covmat-ca.dat
runanalysis diagmatrix matrixdat out evecs-ca.dat vecs 10 name MyEvecs
crdaction CRD1 projection PROJECT modes MyEvecs beg 1 end 2 @CA
runanalysis hist PROJECT:1 PROJECT:2 free 300 out fhist-all.CA.agr bins 400
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Received on Mon Aug 03 2015 - 04:00:02 PDT
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