[AMBER] Principal Component Analysis

From: Beale, John <John.Beale.stlcop.edu>
Date: Wed, 2 Dec 2015 10:23:57 +0000

Amber community,

I need to do principal component analysis on some Amber datasets. I worked through tutorial A22 (Accelerated MD) which gives an example of the use of PCA and a script for processing the data. My script is given below:
cpptraj nac.prmtop <<EOF
trajin nacamd.nc 1 last 1
reference nac.inpcrd
center origin :1-35
image origin center
strip :WAT,Na+
rms reference mass :1-35.CA,C,N out RMSD.out
matrix covar name matrixdat .CA out covmat-ca.dat
analyze matrix matrixdat out evecs-ca.dat vecs 5
analyze matrix matrixdat name evecs-ca vecs 5
analyze modes fluct out analyzemodesflu.dat name evecs-ca beg 1 end 5
analyze modes displ out analyzemodesdis.dat name evecs-ca beg 1 end 5
projection modes evecs-ca.dat out pca12-ca beg 1 end 3 .CA

When I run this cpptraj script, several files are output. Four of them are: RMSD.out, analyzemodesflu.dat, analyzemodesdis.dat, and pca12-ca. The pca12-ca file contains (with my projection settings) three columns of numbers. I can use these to create a contour plot. My question is, which file, analyzemodesflu.dat, analyzemodesdis.dat, or pca12-ca, will have the principal components that I need? Or, do they all represent PCAs for different purposes?


John M. Beale, Jr.
John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy
Saint Louis College of Pharmacy
4588 Parkview Place
Saint Louis, Missouri 63110-1088
Office: 314-446-8461
Cell: 314-315-0409
FAX: 314-446-8460

AMBER mailing list
Received on Wed Dec 02 2015 - 02:30:02 PST
Custom Search