Hi Jason,
I have added the "use_sander=1" in the $general section of input file. However, the computation failed with sander error:
================================================================================
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
sander found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/sander for GB calculations
sander found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/sander for PB calculations
Preparing trajectories for simulation...
50 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
================================================================================
I have serial sander built with gnu compiler.
So, I went into the test folder of Amber11 and did `make test.serial.MM`. It failed at (I wanted to test sander built):
========================================
CALCULATING TEST: 02_MMPBSA_Stability
./Run.mmpbsa.test: Program error
make: *** [test.mm_pbsa] Error 1
========================================
I also did test under $AMBERHOME/AmberTools/test/mmpbsa_py.
It failed at:
===========================
cd 06_NAB_Nmode && ./Run.nmode
diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
...
...
cd 08_Stability && ./Run.stability
./Run.stability: Program error
make: *** [STABILITY] Error 1
===========================
Any idea what's going wrong?
Thank you very much
Ye
On Jul 2, 2011, at 7:18 PM, Jason Swails wrote:
> Hi,
>
> If you have Amber11 available, try setting the variable "use_sander=1" in
> your MMPBSA input file (in the &general section). I'm not sure what's
> happening here, but your filesystem seems to be choking on simultaneous file
> accesses or something like that (perhaps the way NAB handles files is
> causing some grief, maybe you'll have better luck with sander, although it
> will take longer).
>
> HTH,
> Jason
>
> On Fri, Jul 1, 2011 at 5:08 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>
>> 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
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> _______________________________________________
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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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 05 2011 - 10:00:04 PDT
