Hi Dan,
Thanks for the suggestion. However, I tried 'check' command and didn't
have any warnings for those frames. Either in the output file or in the
pdb created from these frames there were no weird issues neither. Could
it be (although for other systems created in the same way everything
worked) that the problem is related to the fact that the ligand is a
branched oligosaccharide? It is the only thing I can think about... That
is the first time I'm doing MM-PBSA free energy decomposition for the
branched saccharides, so I don't know if there could be any potential
problems with them. An another thing I noticed is that although the
complex seems to be very stable in the MD simulation, the total energy
for the complexes, where decomposition didn't work, is 20-30 kcal/mol
(igb=2), whereas for the complexes, where it worked, it is also not
really favourable but at least is in the range of -5 - +5 kcal/mol. For
all of these complexes, I would expect quite nice negative energies
instead based on the way the trajectory looks, on the contacts formed
and on the experimental data (some complexes are taken directly from the
X-ray structures).
Cheers and thank you,
Sergey
On 27.09.2017 19:22, Daniel Roe wrote:
> On Tue, Sep 26, 2017 at 3:13 AM, Sergey Samsonov
> <sergey.samsonov.ug.edu.pl> wrote:
>> "/users/work/czarek/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
>> line 1536, in _get_next_term
>> internal = float(line[11:20])
>> ValueError: could not convert string to float: *********
> I'm not certain, but it seems like maybe an energy value overflowed,
> producing the asterisks. You can check the frames to see if you have
> bad overlaps with the 'check' command from cpptraj (use the GitHub
> version of cpptraj since it has a faster 'check' version).
>
> -Dan
>
>> Exiting. All files have been retained.
>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>> -------------------
>>
>> If I do decomposition on frames one by one separately, it works for some
>> frames without problems but not for others (for the problematic single
>> frames I get the same empty output as shown above). Trajectory
>> (visually) looks fine, there is no sign of corrupted frames, RMSD and
>> other parameters obtained by cpptraj do not seem to be problematic. I
>> tried also to rewrite the trajectory into the the old format but the out
>> come was identical.
>>
>> My input:
>> -------------------------------
>> Input file for GB/decomposition calculation
>> &general
>> startframe=1, endframe=1000, interval=1,
>> verbose=2, keep_files=0,
>> /
>> &gb
>> igb=2,
>> /
>> &decomp
>> idecomp=2
>> /
>> -------------------------------
>> I run MMPBSA in a standard way with all four topogies:
>> MMPBSA.py.MPI -O -i decomp.input -o gb_binding.out -cp complex.top -rp
>> receptor.top -lp ligand.top -sp ../top.top -y ../mdcrd/md.mdcrd
>>
>> Thank you very much and cheers,
>>
>> Sergey
>>
>> --
>> Sergey Samsonov, PhD
>> Project Leader at Laboratory of Molecular Modeling,
>> Department of Theoretical Chemistry,
>> Faculty of Chemistry,
>> University of Gdansk
>> ul. Wita Stwosza 63
>> 80-308 Gdansk, Poland
>> phone: +48 58 523 5166
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Sergey Samsonov, PhD
Project Leader at Laboratory of Molecular Modeling,
Department of Theoretical Chemistry,
Faculty of Chemistry,
University of Gdansk
ul. Wita Stwosza 63
80-308 Gdansk, Poland
phone: +48 58 523 5166
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Received on Thu Sep 28 2017 - 00:30:02 PDT
