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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Received on Mon Apr 19 2021 - 06:30:05 PDT
