Re: [AMBER] 3 trajectory MMPBSA free energy calculation

From: Amy Rice <>
Date: Wed, 10 Aug 2016 10:34:15 -0500

Hi JoAnne,
Have you looked at chapter 31 of the Amber manual? There is a section on
calling from the command line that explains how to give MMPBSA
multiple trajectories: -y for the complex trajectory, -yr to specify the
receptor trajectory, and -yl to specify the ligand trajectory.

On Wed, Aug 10, 2016 at 9:47 AM, JoAnne Babula <> wrote:

> Hello,
> 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 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
> _______________________________________________
> AMBER mailing list

Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
AMBER mailing list
Received on Wed Aug 10 2016 - 09:00:02 PDT
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