[AMBER] Free Energy Landscape for cMD Help

From: bharat lakhani <lakhbharat.gmail.com>
Date: Wed, 17 Jun 2015 22:17:04 -0400

I am trying to calculate Free energy landscape for my bound and unbound
protein species using following script. I have read plenty of AMBER thread
on this but does not seems to get an hold this. Please let me know if this
is a right way of calculating free energy landscape for classical dynamics.
in advance.

ptraj .filename.prmtop <<EOF6 > filename-run6.out
trajin filename.mdcrd.gz 1 49000 1
reference reference.pdb
rms reference .CA mass
projection modes filename-pca100vec.dat out filename_1-10.dat beg 1 end 10

After copying first two PCA modes in to pca12-ca file
readdata pca12-ca

runanalysis hist pca12-ca1:1 pca12-ca1:2 free 300 out fhist-all.gnu bins 400

Then plotting 3D free energy plot from fhist-all.gnu

Bharat Lakhani
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Received on Wed Jun 17 2015 - 19:30:02 PDT
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