Re: [AMBER] Very low MMPBSA result

From: David A Case <>
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.


AMBER mailing list
Received on Sat Apr 11 2020 - 05:30:03 PDT
Custom Search