Re: [AMBER] PCA analysis

From: Elvis Martis <>
Date: Thu, 9 Feb 2017 15:02:25 +0000

Cpptraj can very well do PCA.
The script you have will work will CPPTRAJ.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Thakur, Abhishek []
Sent: Thursday, February 09, 2017 8:28 PM
Subject: [AMBER] PCA analysis

Hi everyone,

It is my first time for PCA analysis

I have figured out my script, can anyone help me out how to analysis it after running following scrip. Do I need some other software to analyze it?

trajin PRMT7_ILE71_aMD_0_300ns.crd.gz
# Fit to first frame for averaging
rms first .CA
# Average the trajectory
average PRMT7_ILE71_aMD_avg_pdb.pdb pdb
# Save the rms-fit coords
createcrd crd1
# First run
# Load the generated average as reference reference PRMT7_ILE71_aMD_avg_pdb.pdb # Fit saved coords to the reference crdaction crd1 rms reference .CA # Calculate covariance matrix from fit coords crdaction crd1 matrix out matrix.dat name mymatrix covar .CA # Diagonalize matrix to get eigenvectors/eigenvalues runanalysis diagmatrix mymatrix out evecs.dat vecs 20 name mymode # Project fit coords along eigenvectors 1-3 crdaction crd1 projection myproj modes mymode out projection1-3.out beg 1 end 3 .CA # Set up hitograms for PC projections multihist myproj bins 200 normint out PC.multi.hist.agr #hist myproj:2 bins 200 normint out PC.hist.2.agr #hist myproj:3 bins 200 normint out PC.his.3.agr # Run analyses runanalysis

Thanking you,


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