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.
Thanks
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
.CA
EOF6
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
--
regards
Bharat Lakhani
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Received on Wed Jun 17 2015 - 19:30:02 PDT
