[AMBER] MM/PBSA and GBSA fails

From: Thakur, Abhishek <axt651.miami.edu>
Date: Sun, 7 Jun 2020 23:02:48 +0000

Hi everyone,

I have a complex system for which I am trying to compute the binding affinity over 500 ns of simulation by MM/PBSA and MM/GBSA method.
Unfortunately, the binding affinity predicted is very high, i.e., DELTA TOTAL = 693215.1234 Kcal/mol for one system but for other systems binding affinity seems to be reasonable ~ -21 Kcal/mol.
An interesting thing is that ligand is the same but protein is different isoform and experimentally this system should be the best binder.
Any suggestions on how to tackle this problem will be highly appreciated.
Is there any other technique that I can apply using the 500ns MD trajectory?

with regards,

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Received on Sun Jun 07 2020 - 16:30:02 PDT
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