[AMBER] PCA and motions visualization

From: <antonio.coluccia.uniroma1.it>
Date: Tue, 21 Jul 2015 11:59:54 +0200

Dear amber user's

I would like to visualize the result of the pca analyses on my
trajectories.
Following instructions founded at this tutorial :
http://spider.irb.hr/tutorial2/Tutorial2.htm#_B%29_Principal_Component_Analysis
i was able to produce the covariance matrix and then to compute the
eigenvector and the eigenvalue. I have obtained that the first two
eigenvectors share the 70% of the information.
I have projected the trajectory along the first two PCs obtaining a file
with mode1 and mode2.
I this point I would like to visualize the protein movements for both
the PCs.

Does it exist a way to write the trajectories corresponding to each of
the studied PCs and then to visualize them by VMD or other software; and
is it the right way to draw a porcupine plot?

I don't know how to manage these steps

Attached you will find the script used

parm complex_wt_rs.prmtop

trajin md.mdcrd

center origin :1-982

image origin center

reference complex_wt_rs.inpcrd

rms reference mass :1-982&!.H out rmsd.csv

atomicfluct out RMSF.csv :1-982&!.H byres

trajout md_fitted.mdcrd

strip :WAT,Na+

trajout md_fitted_stripped.mdcrd

run

trajin md_fitted.mdcrd

matrix covar name matrixdat @CA out covmat.dat

analyze matrix matrixdat out evecs.dat vecs 15 name myEvecs matrix

analyze matrix matrixdat name evecs-ca vecs 15

projection P1 modes evecs.dat out pca12.dat beg 1 end 2 @CA

run


Best regards


Antonio

-- 
Antonio Coluccia, Ph.D.
Department of Chemistry and Drugs Tecnology
La Sapienza University
Rome 00185
Piazzale Aldo Moro 5
antonio.coluccia.uniroma1.it
mobile: 00393406113351
-- 
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Received on Tue Jul 21 2015 - 03:30:03 PDT
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