You've touched on another issue that is actually solved with the upcoming
MMPBSA.py release (this is, IMO, one of the largest shortcomings of the
current version). The only way DELTA decomposition energies can be
calculated is if we know "residue mapping". That is, if we know where
every residue is *exactly* in both the complex and [receptor or ligand]
topology files. Only then can you subtract the two of them. The perl
version required 2 extra input variables: RECMAP and LIGMAP -- that is, you
have to directly tell mm_pbsa.pl where the complex residues "map" onto the
receptor and ligand residues. This is difficult to wrap your head around,
IMO, and very easily leads to user errors that very easily slip through the
mesh, so we decided not to take that approach.
When MMPBSA.py determines the receptor and ligand masks, it maps out the
residue correspondence (mapping) in the process. The decomp parsing code
takes advantage of this to calculate the deltas appropriately. If users
supply their own masks for the receptor and ligand, this mapping doesn't
take place, so the decomp parser has no idea what differences to take for
each residue. Thus, that check is very much important.
I've implemented a mask parser written in Python for the upcoming MMPBSA.py
release, however, which solves this problem. When it interprets the
receptor and ligand masks, it maps out which atoms belong to the receptor
and which belong to the ligand, which serves 2 purposes. First, we now
*always* have the mapping necessary to calculate decomp DELTAs, and second,
it's an additional layer of error checking to make sure that the masks
users input are not wrong.
All the best,
Jason
On Fri, Nov 4, 2011 at 12:47 PM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Huhu,
>
> once again me. Sorry :)
>
> I've performed two equivalent MMPBSA.py.MPI runs. One with
>
> dec_verbose=0
>
> and one with
>
> dec_verbose=3
>
> In both cases, the DELTA section was not written in
> FINAL_DECOMP_MMPBSA.dat. But only in the first case, this message is
> printed to FINAL_DECOMP_MMPBSA.dat:
>
> "DELTAs can only be printed with the default mask assignments"
>
> I am wondering if these lines:
>
> > if ligstart == -1 and verbose <= 2 and not stability:
> > output.write("DELTAs can only be printed with the default mask
> assignments\n\n")
> > verbose += 2
>
> in AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py really make
> sense (especially the condition `verbose <= 2`). Do they? :)
>
> Thanks,
>
> Jan-Philip
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Nov 04 2011 - 13:30:03 PDT
