Well, it appears that you do have a different issue ... maybe somebody
else can help further. From the error you report its not easy to guess
what the issue is .... Are your input files OK? Can you perform your
PB/GB calculations separately with "sander" ? What are your "mdout"
files saying, any hint there ? Probably you need to go step by step
manually in the MMPBSA procedure with full verbose output and try to
figure out where things go wrong ....
Sorry for not being so helpful ....
Good luck !
On 01/31/2017 02:38 PM, Albert wrote:
> Even I calculated MM/PBSA with single CPU, it failed with similar messages:
>
> ----------------------
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /soft/amber/16/bin/mmpbsa_py_energy
> cpptraj found! Using /soft/amber/16/bin/cpptraj
> Preparing trajectories for simulation...
> 100 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /soft/amber/16/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/soft/amber/16/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /soft/amber/16/bin/mmpbsa_py_energy failed with prmtop
> com.prmtop!
> Exiting. All files have been retained.
>
>
>
>
>
> On 01/31/2017 10:38 AM, Vlad Cojocaru wrote:
>> One job meaning a single MPI process, or a single job with multiple MPI
>> processes ?
>>
>> Depending on the system size, grid size and number of MPI processes
>> asked in 1 job, you may easily consume 64 GB .. At least that was the
>> case with Amber 12 and 14 ... I know that in Amber 16 a lot of
>> optimizations were done with the MMPBSA code, but we have limited
>> experience thus far with Amber 16 and MMPBSA.
>>
>> All I can say is that we experienced this error often in this context
>> before ... But I also know this is a generic error that can be due to
>> multiple other reasons ... So, if you calculated your memory consumption
>> and you found is fine within your limits, you would have to search for
>> other potential issues ...
>
>
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>
--
Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Tue Jan 31 2017 - 06:30:04 PST
