Thanks for the long comment, Jason!
First, I have to add that maybe the subject of my mail was misleading. I
did not question the check itself. The way I had set up the system,
MMPBSA.py did not determine the receptor and ligand masks automatically
and therefore the warning
> "DELTAs can only be printed with the default mask assignments"
should have been printed to the output file. Especially, it should have
been printed independently of the dec_verbose setting, right?
In my case, it only happened for dec_verbose = 0. I did not have this
warning in the output file for dec_verbose = 3. At this point I am
wondering if it makes sense and this is why I questioned the Python
condition `and verbose<= 2`, which limits the cases for printing this
warning.
Second, what you've written sounds very reasonable. But, just in order
to make sure I got you right:
- in case MMPBSA.py determines the ligand and receptor masks from the
topology files, these masks are "forwarded" to the "decomp parsing code"
- in case the user defines ligand and receptor masks in the MMPBSA input
file, these masks are considered to be not trustworthy enough to be
"forwarded" to the "decomp parsing code"
Is that somehow correct?
Third, a totally different thing on MMPBSA.py which I was wondering
about for some time now but maybe it's not worth opening a new topic for
that. The level of parallelization of MMPBSA happens on the level of
different frames, i.e. several workers work on different frames, right?
The analysis of a single frame is not worth to further split and
parallalize. Hence, the serial version of ptraj is used for frame
extraction and the serial version of sander is used for frame analysis.
These processes need to be managed by Python in a parallel fashion. My
point is: I do not quite get why MPI is used for that. I must be missing
something, otherwise this process management could easily be done using
Python's multiprocessing module. Must MMPBSA.py be able to work
distributed over various nodes?
Hopefully my mails don't annoy you :)
Have a nice weekend!
Jan-Philip
On 04.11.2011 21:00, Jason Swails wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Fri Nov 04 2011 - 14:00:03 PDT
