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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 11 2020 - 05:30:03 PDT
