Based on what you've said, I would guess there is an issue with your
simulation and not the free energy calculations. I would suggest
visualizing your trajectory closely. Additionally, you should look at the
binding free energy as a function of time. It is possible that a
problem occurred during a single frame that might have increased the
standard deviation and avg free energy substantially. Could be an
indication of an issue with the application of a force field to part of
your system.
-Bill
On Thu, Sep 7, 2023 at 3:39 AM Kankana Bhattacharjee via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER users,
>
> I have performed protein-ligand binding affinity using MMPBSA using amber
> 22 version. I did the analysis for the 200 and 2000 frames from the last 20
> ns. I am trying to reproduce one paper's result. In case of 200 frames
> contribution matched closely with reference result but, while using 2000
> frames, standard deviation is found to be extremely high (~+-50-100) !!
> Also, free energy of binding is found to be comparatively higher than the
> actual result.Single trajectory approach is used and one complex trajectory
> is used for the MMPBSA analysis.
> Kindly suggest me regatrding the issue. Should multiple complex simulations
> have to be performed ?
>
> Thanks & Regards
> Kankana Bhattacharjee
> Ph.D. Scholar
> Department of Chemistry
> Ashoka University
> Sonipat, Haryana
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>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Thu Sep 07 2023 - 12:00:02 PDT
