Re: [AMBER] Regarding entropy calculations in when enthalpy is either from GBSA or PBSA?

From: David A Case <>
Date: Sun, 17 Oct 2021 06:34:32 -0400

On Sat, Oct 16, 2021, Liao wrote:
>Are people using the exact same nmode (or quasi harmonic) entropy, whether
>the H is from MMPBSA or MMGBSA? Because their H values are quite different.

Large differences between GB and PBSA are worth looking into. The most
usual explanation is that you are using different radii in the two
calculations, but other explanations are possible.

It's hard to say much since we have no idea of what sort of system you are
looking at, how different the GB and PB results are, and what options you
gave to the program.

People should remember that all free energy calculations are advanced
topics: be sure that you have run some simple systems and are confident in
analyzing those, before tackling more complex problems.


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Received on Sun Oct 17 2021 - 04:00:03 PDT
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