Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 19 Apr 2021 19:40:59 +0530

Dear David,
I have a total of 2000 frames in the trajectory.
How many would you consider sufficient for this type of complex with a
total of 234 residues?
I tried the nmode calculation with 2 frames but it did not print the final
results and exited without any error message.
I will try to reproduce that, check for any printed error messages and post
them here soon for further advice.

Thanks a lot for useful comments and suggestions.
Best regards.
Vaibhav

On Mon, Apr 19, 2021 at 6:48 PM David A Case <david.case.rutgers.edu> wrote:

> On Sun, Apr 18, 2021, Vaibhav Dixit wrote:
>
> >I'm getting very high entropy values after running the MMPBSA with the
> >following input.
>
> Quasi-harmonic entropies are very difficult to converge. I would think
> that
> using only 400 frames is way too few. Have you tried doing the entropy
> calculation (only) with many more frames? [You don't need the MMPBSA.py
> program here--just use cpptraj.]
>
> Also, try using the normal mode model (you generally would not need very
> many frames here, but you can check to see what the difference is from one
> frame to the next.) When things are working and converged, the two
> estimates should not vary by a lot. If you have a weak binding affinity,
> you are facing a problem that may require a lot of careful attention to get
> reliable answers.
>
> ...dac
>
>
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-- 
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
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Received on Mon Apr 19 2021 - 07:30:03 PDT
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