[AMBER] PCA analysis

From: Thakur, Abhishek <axt651.miami.edu>
Date: Thu, 9 Feb 2017 14:58:24 +0000

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

Thanking you,


AMBER mailing list
Received on Thu Feb 09 2017 - 07:00:03 PST
Custom Search