Just finishing some tests I got the error on the step of the
calculation of dG for the complex:
Line minimizer aborted: step at upper bound 0.14208831
File "/home/gleb/amber22/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/home/gleb/amber22/lib/python3.9/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/gleb/amber22/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/gleb/amber22/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
line 321, in run
Calculation.run(self, rank, stdout=self.output % rank)
File "/home/gleb/amber22/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/gleb/amber22/bin/mmpbsa_py_nabnmode failed with
prmtop complex.prmtop!
Error occurred on rank 46.
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 46
may it be related to the open mpi problem or rather something wrong
with the system ( I run it on the system that had not been
reimaged..)?
Il giorno lun 8 ago 2022 alle ore 19:20 Ray Luo <rluo.uci.edu> ha scritto:
>
> Hi Enrico,
>
> Here are my suggestions regarding your questions ...
>
> > 1) Dealing with the modeling of the dimeric protein where the ligand
> > is bound to one of the monomers, do I need to re-image my system prior
> > to the post-processing (avoiding jumping parts of the protein across
> > the PB) ?
>
> Yes you'll need to make sure all proteins are in the primary cell
> before stripping waters/ions etc. To make sure the system looks right,
> I strongly recommend visualizing the stripped trajectories before
> running the job.
>
> > 2) What snapshot density is required for the calculations? For
> > example, dealing with the 150ns trajectory where each snapshot was
> > saved every 25000 steps, I have around 6000 snapshots. In order to
> > speed up the analysis, would it be OK to take each 5th snapshot for
> > the calculations of dH and each 10th for the dS ?
>
> In general, you can use fewer snapshots to save time. The con is that
> you'd get higher uncertainties, i.e. standard errors.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Mon, Aug 8, 2022 at 7:49 AM Enrico Martinez via AMBER
> <amber.ambermd.org> wrote:
> >
> > Here is my script
> > &general
> > startframe= 1, interval=${int}, keep_files=2,
> > strip_mask=:WAT:Cl-:Na+:K+, netcdf=1
> > /
> > &gb
> > igb=5, saltcon=0.150,
> > /
> > &nmode
> > nmstartframe=1, nminterval=5, nmode_igb=1, drms=0.05, nmode_istrng=0.15,
> > /
> > &decomp
> > idecomp=1,
> > dec_verbose=1,
> > /
> >
> > Many thanks in advance!
> > Cheers
> > Enrico
> >
> > _______________________________________________
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> > AMBER.ambermd.org
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Received on Tue Aug 09 2022 - 00:30:04 PDT
