Hi Jason,
The serial version is only having some minor issues.
Following is the output:
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
mmpbsa_py_energy found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for GB calculations
mmpbsa_py_energy found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for PB calculations
Preparing trajectories for simulation...
50 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with mmpbsa_py_energy...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with mmpbsa_py_energy...
calculating complex contribution...
PB Info in pb_read(): npopt has been overwritten with inp
Total surface charge 2.9598
Reaction field energy -4821.5307
Cavity solvation energy 77.1504
...
...
Reaction field energy -4763.0697
Cavity solvation energy 78.8077
calculating receptor contribution...
PB Info in pb_read(): npopt has been overwritten with inp
Total surface charge 1.9721
Reaction field energy -3552.3284
...
...
Reaction field energy -5066.6010
Cavity solvation energy 62.5406
calculating ligand contribution...
PB Info in pb_read(): npopt has been overwritten with inp
Total surface charge 0.9867
Reaction field energy -2684.2835
...
...
Reaction field energy -2737.6791
Cavity solvation energy 34.1780
Timing:
Total setup time: 0.031 min.
Creating trajectories with Ptraj: 0.084 min.
Total calculation time: 29.421 min.
Total GB calculation time (sander): 1.623 min.
Total PB calculation time (sander): 27.798 min.
Statistics calculation & output writing: 0.002 min.
Total time taken: 29.538 min.
MMPBSA.py Finished! Thank you for using. Please report any bugs to amber.ambermd.org
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Thanks
Ye
On Jul 1, 2011, at 11:39 AM, Jason Swails wrote:
> Does it work in serial if you test it on just the first couple frames?
>
> On Fri, Jul 1, 2011 at 10:00 AM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>
>> Hi,
>>
>> I came across some errors when running MMPBSA.MPI. Following is the output:
>>
>>
>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
>> Running MMPBSA.MPI on 4 processors...
>> Reading command-line arguments and input files...
>> Loading and checking parameter files for compatibility...
>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
>> mmpbsa_py_energy found! Using
>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for GB calculations
>> mmpbsa_py_energy found! Using
>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for PB calculations
>> Preparing trajectories for simulation...
>> 2150 frames were read in and processed by ptraj for use in calculation.
>>
>> Beginning GB calculations with mmpbsa_py_energy...
>> calculating complex contribution...
>> calculating receptor contribution...
>> calculating ligand contribution...
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>>
>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> I have AmberTool 1.5 with Amber 11 fully patched and compiled with gnu
>> compiler. Mpi4py is built with openmpi-1.4.3.
>>
>> Any idea what's going wrong?
>>
>> Thanks
>> Ye
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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>
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Received on Fri Jul 01 2011 - 16:30:03 PDT
