Re: [AMBER] Extracting total energy and other enegy componenets of ligand

From: Daniel Roe <>
Date: Wed, 2 Jul 2014 08:20:21 -0600


You could potentially strip everything but the ligand from your trajectory,
then perform energy post-processing with sander (imin=5) to obtain the
potential energy terms for only the ligand. A few caveats with this: 1) You
won't get kinetic energy from this, and if you didn't save velocity
information there is no way to calculate the kinetic energy of the ligand
(assuming you haven't saved your trajectory every timestep), and 2) the
energies you obtain with imin=5 will be slightly off from what is in your
output file, which is expected (the output file energies are always 1
timestep behind coordinates).

Hope this helps,


On Wed, Jul 2, 2014 at 3:51 AM, Soumendranath Bhakat <> wrote:

> Dear All;
> We are running a typical protein-ligand simulation in explict solvation. As
> we know that the total, kinetic and potential energy parameters will be
> written in md.out file and can be extracted by some perl script. But the
> total energy or the potential or knetic energy parametrs coming from a
> md.out is taking in account receptor+ligand+solvation term.
> My question is I want to calculate potential, kinetic/total energy terms
> coming from the ligand component.
> Is there any way to know whats the energy component coming from the ligand
> in
> --
> Thanks & Regards;
> Soumendranath Bhakat
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jul 02 2014 - 07:30:05 PDT
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