On Fri, Oct 30, 2015 at 6:52 AM, MarcZhang <progress0935zhang.gmail.com>
wrote:
> Dear Amber user group
>
>
>
> I would like to estimate the contributions of residues in the pocket to
> ligand binding by decomposing deltaG onto each residue using MMPBSA.py
>
>
>
> However, the calculation of decomposition cannot be completed. Could
> someone
> tell me why it is?
>
I *suspect* that is because for pairwise decomposition, each residue pair
requires its own, separate PB calculation. The PB energy expression really
has no parts that are easily decomposed into pairwise interactions.
I would typically not recommend using PB for pairwise decomposition
(per-residue decomposition probably wouldn't be as bad).
Does amber have any other module/script for energy decomposition?
>
Not if you want to include solvation effects through GB or PB. But GB
decomposition is a *lot* faster (about the same speed as "regular" GB
without decomposing per-residue contributions).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 30 2015 - 07:30:03 PDT
