Hi Tue,
The decomposition code has not changed in years.
It's unclear to me exactly what you're observing (which is why sending
actual output/files is so helpful). Examples of the questions I have are
posted in-line
On Sun, Feb 13, 2022 at 9:47 PM Tue Boesen <alyflex.gmail.com> wrote:
> I believe there is a bug when running mmpbsa with idecomp setup for
> pairwise energies (idecomp=3 or idecomp=4).
>
> In this mode the internal energies are reported at zero, while all other
> energies are given with reasonable values that add up to their total value
> and matches the results you would get if you ran it with idecomp=1-2 (per
> residue).
>
What values are you looking at? The complex/receptor/ligand, or the
binding totals (that is, the difference between the bound and free
states)? All of them?
For instance, the internal terms *should* always be zero for total binding
terms in a single-trajectory protocol, since the bonded geometries are
identical in the bound and unbound states. They are also likely to be very
close to zero in the residue-pairwise decomposition, since only those terms
that bridge two residues would actually contribute to this term, and if
they are close to equilibrium values the total energies will not be very
large.
I also don't understand what you mean by "matches the results you would get
if you ran it with idecomp=1,2". These compute fundamentally different
quantities, so the numbers should be quite different. The Amber force
field potential is not pairwise decomposable, so idecomp=3,4 are only
approximations, anyway.
The error appears in both the csv, and final decomposition output and means
> that the energies do not add up as they are supposed to. The energies in
> FINAL_RESULTS_MMPBSA, still include the summed total of the internal
> energies, and give identical results as when ran with idecomp=1-2.
>
How do you expect the terms to add up? This is where actual output files
and precise descriptions help.
Good luck,
Jason
--
Jason M. Swails
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Received on Thu Feb 17 2022 - 07:30:02 PST
