Just to pitch in that if it's failing at igb=5 and not igb=1, it might be a
radii issue since I think the 1 and 5 options treat atomic radii
differently. But again, that's entirely speculation and not much use
without checking the mdout.
Best,
Kenneth
On Fri, Mar 27, 2015 at 1:56 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> > On Mar 27, 2015, at 12:39 PM, Abhishek Tyagi <atyagiaa.connect.ust.hk>
> wrote:
> >
> > Hi,
> >
> > this is running on gnu cluster on serial installation, I found that for
> the first problem when i set igb=1, MMGBSA is running, but when it is set
> igb=5, it shows the error
> >
> > File "/ghome/atyagiaa/amber14/bin/MMPBSA.py", line 96, in <module>
> > app.run_mmpbsa()
> > File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/main.py", line 218, in
> run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/calculation.py", line 79, in
> run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/calculation.py", line 148,
> in run
> > self.prmtop))
> > CalcError: /ghome/atyagiaa/amber14/bin/sander failed with prmtop
> complex.prmtop!
> > Exiting. All files have been retained.
>
> Look in the Mdout file as Kenneth suggested. It is likely that an error
> message was printed there. All that you've told us here is that something
> went wrong.
>
> > for the second problem: I have followed the installation guide as
> follows:
> >
> > ./configure -mpi gnu
> > make install
> > export DO_PARALLEL='mpirun -np 16’
> > make test.parallel
> >
> > everything finished fine, but when I had checked AMBERHOME/bin/ their is
> no MMPBSA.py.MPI file in the folder.
> >
> > what could be the reason
>
> Maybe mpi4py did not install correctly. Did you see a message about that
> in the build log? If the mpi4py build fails, I don't think MMPBSA.py.MPI
> will be installed.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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here could not dream of heaven?
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Received on Fri Mar 27 2015 - 16:00:03 PDT
