Re: [AMBER] mmpbsa

From: Chris Moth <>
Date: Tue, 9 Apr 2019 21:30:18 -0500

I don't think that "motion of ligand to protein" is desirable with
MMPBSA, which is calculated from an equilibrium trajectory.

Be sure to run through a tutorial:

I recall that lack of treatment of Entropy can be an issue, also length
of the equilibrium trajectory.

Good luck.  (It's been a few years since I tried this technique -
apologies in advance if I have been unhelpful).

On 4/9/2019 3:22 AM, MYRIAN TORRES RICO wrote:
> Hi all,
> I wanted to ask you a question about the mmpbsa program. I have
> performed my dynamics in my complexes and when I have done my
> calculations of mmpbsa on my files of final coordinates, I have
> obtained in the decomposition energy table, interactions in areas of
> the protein that in principle my ligand has not moved to them nor
> nothing ... I've visualized it and it's not even close ... How is it
> possible that I do this ...?
> Thanks in advance!
> Kinds regards,
> Myriam
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Received on Tue Apr 09 2019 - 20:00:02 PDT
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