[AMBER] cpptraj PCA of crystal structure

From: anu chandra <anu80125.gmail.com>
Date: Thu, 5 Jan 2017 16:25:48 +0000

Hello all,

I am trying to project the crystal structure of a protein with 210
aminoacids, into top two PC (principle component) space. For this, I have
carried out PCA of crystal structure with the following script.
Unfortunately, all modes came out as zeros. The crystal structure was
obtained from PDB. Am I doing anything wrong here?.

parm 1atm.pdb

trajin 1atm.pdb

createcrd crd1

crdaction crd1 matrix covar !.H= name gaccCovar

runanalysis diagmatrix gaccCovar vecs 2 name evecs

crdaction crd1 projection T1 modes evecs beg 1 end 2 !.H= out T1.dat

Any help would be highly appreciated

Many thanks
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Received on Thu Jan 05 2017 - 08:30:03 PST
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