I want to run the bennett.py script manually to perform analysis on a subset of frames. How can I do that?

To run the bennett.py script manually, you will need to locate, collect, and rename a few files. First, you will need to find the .dE files from the production run trajectory, which should be stage 11. That is, you need to unpack the following .tgz file:

jobname_11-out.tgz

Inside, you will need to locate the .dE files, which are named according this scheme:

jobname_11_lambdalambda#.lambda#.dE

Copy all of these files into a new directory, and rename the files according to this scheme:

gibbs.lambda_#.dE

You can then run bennett.py using a command like the following:

$SCHRODINGER/run -FROM desmond bennett.py -b 150.0 -e 600.0 -F 2 -R 1 -T 298.15 -s gibbs.%d.dE -l 0 -L 11 -o 150_600.result

This will instruct bennett.py to estimate the dG values for the time range from 150 to 600 ps. The flag -F and -R correspond to the forward (-F) and reverse (-R) mutations.

The command assumes that there are 12 lambda windows labeled from 0 to 11.

Keywords: Desmond, MD analysis, bennett

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