[AMBER] 3 trajectory MMPBSA free energy calculation

From: JoAnne Babula <jbabula.umail.iu.edu>
Date: Wed, 10 Aug 2016 10:47:45 -0400


      I would like to calculate the binding and total free energy for a
complex using AMBER14, but I would like to use 3 separate simulations to do
so, one with the ligand alone, one with the protein alone, and one of the
complex. I need to use three separate trajectories because the protein I am
using undergoes a conformational change when bound by the ligand, so using
the complex simulation alone does not deliver an accurate assessment of
total free energy change. I am not certain how to specify that I would like
the MMPBSA program to use 3 separate mdcrd files.
     I have also noticed the FEW.pl program may be able to separately
calculate free energy for each simulation, but FEW also requires that the
simulations be generated through its workflow, and since I already have the
3 simulations I would like to use, I would like to avoid this extra effort.
Can you suggest a course of action? Thank you so much.

Very Respectfully,
JoAnne J Babula
Ph.D. Candidate, IUSM, Dept. of Pharmacology
U.S. Army, 1LT, MS
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Received on Wed Aug 10 2016 - 08:00:02 PDT
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