[AMBER] MM/PBSA after minimization

From: <h_sahakyan.mb.sci.am>
Date: Mon, 02 Nov 2020 19:12:00 +0000

Dear Dr. Case,

I understand that MM/GBSA is designed to calculate energies using MD snapshots. Nevertheless, I would like to use it for docking results rescoring and any recommendations will be very much appreciated.
The initial benchmarks demonstrated that it works and improves AUC and Enrichment factor, though in the case of some proteins it fails. Interestingly, I noticed that minimization using just 500-1000 steps yields better results than full minimization (with drms = 1.0E-4 for example). What do you think about it?

Best wishes,
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Received on Mon Nov 02 2020 - 11:30:03 PST
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