Dear Friends!
Well, I still have problems with MMPBSA.py
Firstly I created stripped topologies using
ante-MMPBSA.py -p ${sim}/protein.prmtop -c ${sim}/protein.prmcrd -c
complex.prmtop -r receptor.prmtop -l ligand.prmtop -s :WAT:Cl-:Na+:K+
-n :lig > ante_${simulation}.log
Then I checked all stripped topologies and trajectories, and
everything was correct.
Finally I run mmpbsa.py.MPI with this script:
&general
startframe= 1, interval=10, keep_files=2, entropy=1, netcdf=1
/
&gb
igb=5, saltcon=0.150,
/
&decomp
idecomp=1,
dec_verbose=1,
print_res="142,145,163,166,189"
/
1) When I do calculations without entropy (entropy=0), everything goes OK!
2) when I add entropy=1 option to & general, it produces the following error:
Error: PDB _MMPBSA_avgcomplex.pdb: No frames read. atom=8849 expected 9333.
Error: Could not set up '_MMPBSA_avgcomplex.pdb' for reading.
Error: DataSet_Coords_REF: Could not set up trajectory.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
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 375, in run
Calculation.run(self, rank, stdout=self.output)
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/cpptraj failed with prmtop complex.prmtop!
Error occurred on rank 68.
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 68
although I've mentioned the same script without entropy computing
(using the same inputs) works perfectly...
3) In the case of entropy computing using NMA, I have another error
mentioned earlier. How would it be possible to debug my system
assuming that I've already double-checked all generated topologies and
trajectories?
Many thanks in advance!
Enrico
Il giorno mar 9 ago 2022 alle ore 16:31 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> Right, thank you!
> I am going to carry out some tests, I suppose the problem was related
> to the re-imaging of the system. Otherwise, what options may be useful
> for NMA section to overcome problems related to minimization?
> Cheers,
> Enrico
>
> Il giorno mar 9 ago 2022 alle ore 16:17 Ray Luo <rluo.uci.edu> ha scritto:
> >
> > Enrico,
> >
> > "Line minimizer aborted" is related to your nmode option, so I don't
> > think it's MPI related. You may want to test run a few snapshots with
> > the serial mode to make sure the setup is correct before the MPI
> > production run.
> >
> > Finally, please make sure your systems are correctly stripped before
> > running again.
> >
> > 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 Tue, Aug 9, 2022 at 12:13 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
> > >
> > > 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
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
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Received on Wed Aug 10 2022 - 02:30:03 PDT
