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?.
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parm 1atm.pdb
trajin 1atm.pdb
createcrd crd1
run
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
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Any help would be highly appreciated
Many thanks
Anu
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Received on Thu Jan 05 2017 - 08:30:03 PST
