Re: [AMBER] Very low MMPBSA result

From: David A Case <david.case.rutgers.edu>
Date: Sat, 11 Apr 2020 08:00:25 -0400

On Sat, Apr 11, 2020, Nada Afiva wrote:

>Yes I am using the single-trajectory approach.

If you use the single-trajectory approach, then the bond energy
contribution to binding should be zero. Try a very short simlation,
even one frame: since you have saved the intermediate files, just do a
single-step calculation (by hand) on receptor, ligand and complex, and
do the delta calculations yourself. You may be able to see what is
going wrong.

....dac


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Received on Sat Apr 11 2020 - 05:30:03 PDT
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