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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Received on Wed Aug 20 2014 - 10:00:03 PDT
