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
