Re: [AMBER] Interpreting MM-(GB)PBSA results

From: David A Case <>
Date: Mon, 28 Jan 2019 07:54:33 -0500

On Sat, Jan 26, 2019, Sundar wrote:
>I am performing MMPBSA and MMGBSA calculations for a protein-ligand
>complex. Protein is small, containing 50 residues. GBSA is giving a Delta
>Total of -5.2 and PBSA is giving 0.34 kcal/mol. How to interpret the
>difference between these numbers? Why's GBSA binding affinity is stronger
>than PBSA?

This is not an unusual difference. You might read various reviews on
MM/PB(GB)SA end point methods. It is in general much harder to get
useful quantitative results than many new users expect.

>How long should be the simulation to get reliable results? How do I measure
>the convergence?
>Do multiple replicates of the simulation help to improve the accuracy?
>What if the ligand leaves the binding site during the simulation? Can I
>include those frames as well in these binding affinity calculations? If
>not, can I use some restraints to keep the protein-ligand bound together?

Above are good questions, but not ones that can be easily answered on a
mailing list, since there probably are no general answers. Don't be
afraid to experiment. If you ligand is not stable in the binding site,
then the assumption that you can correctly sample configurations from
the end-point "bound" state is probably not valid.


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Received on Mon Jan 28 2019 - 05:00:03 PST
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