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

From: David A Case <david.case.rutgers.edu>
Date: Tue, 20 Apr 2021 07:58:48 -0400

On Tue, Apr 20, 2021, Vaibhav Dixit wrote:

>This seems like a very large number of frames and thus bring some questions
>to mind.
>At present I have 2000 frames for a 40 ns simulation, thus what would you
>recommend?

I don't think it's very feasible to use quasiharmonic calculations to
estimate entropy on a 234-residue protein. It's probably possible to make
some approximations (e.g. don't compute all the modes), but this would be a
research project in itself, and one would need to understand in detail what
quasiharmonic calculations are doing.

>Also, it will be helpful if you can suggest how to troubleshoot the mode
>calculation especially in the absence of useful error messages.

Please re-read the opening paragraphs of the MMPBSA.py chapter, especially
the part in bold-face type. Also, I can't remember if you confirmed that
you looked in all the output files to find possible error messages.

...dac


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 20 2021 - 05:00:02 PDT
Custom Search