No I didn't get any other error message. So why do you think I might be
getting
CalcError: /global/software/amber/amber14/bin/sander failed with prmtop
./nw.complex.top!
?
--Holly
On Wed, Aug 20, 2014 at 10:56 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Aug 20, 2014 at 12:44 PM, Hallel Freedman <hfreedma.ualberta.ca>
> wrote:
>
> > Hi Jason,
> >
> > I updated to AMBER14Tools and I am still getting an error.
> > This time:
> > File "/global/software/amber/amber14/bin/MMPBSA.py", line 96, in ?
> > app.run_mmpbsa()
> > File "/lustre/jasper/software/amber/amber14/bin/MMPBSA_mods/main.py",
> > line 218, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File
> > "/lustre/jasper/software/amber/amber14/bin/MMPBSA_mods/calculation.py",
> > line 79, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> > "/lustre/jasper/software/amber/amber14/bin/MMPBSA_mods/calculation.py",
> > line 147, in run
> > raise CalcError('%s failed with prmtop %s!' % (self.program,
> > CalcError: /global/software/amber/amber14/bin/sander failed with prmtop
> > ./nw.complex.top!
> > Exiting. All files have been retained.
> >
> > My system contains MNG and so I tried once stripping MNG and once without
> > stripping it, and either way I get the same error. Should it be necessary
> > to strip the Manganese ions?
> >
>
> The GB models have not been parametrized for Manganese, so I would be
> careful about interpreting these results.
>
> All you reported here was the stack trace printed by MMPBSA.py -- I didn't
> see an actual error message (was there one?). Did you still get a message
> about a radius not being found?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Wed Aug 20 2014 - 10:30:02 PDT
