[AMBER] Suggestions on MM-(GB)PBSA

From: Sundar <jubilantsundar.gmail.com>
Date: Tue, 22 Jan 2019 01:20:56 -0600

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?

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?

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Received on Mon Jan 21 2019 - 23:30:03 PST
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