Hi Bill,
This is the last part of _MMPBSA_receptor_pb.mdout file:
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1
Total surface charge 1.9723
Reaction field energy -3570.1196
Cavity solvation energy 54.6777
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.1384E+03 1.7292E+01 1.0289E+02 N 680
BOND = 329.2644 ANGLE = 939.0290 DIHED = 1182.0229
VDWAALS = -670.5602 EEL = -7995.5664 EPB = -3570.1813
1-4 VDW = 394.1857 1-4 EEL = 6198.7732 RESTRAINT = 0.0000
ECAVITY = 54.6777 EDISPER = 0.0000
minimization completed, ENE= -.31383551E+04 RMS= 0.172922E+02
minimizing coord set # 2
67.611999999999995 5.7789999999999999 0.63300000000000001
pb_fdfrc(): Atom out of focusing box 251 59 44
------------------------------------------------------------------------------------------------------------------------
I hope it helps.
Thanks
Ye
On Jul 5, 2011, at 11:57 AM, Bill Miller III wrote:
> What is at the end of the _MMPBSA_receptor_pb.mdout file? There should be an
> error message or warning in that file that should help explain the error
> based on where the calculation ended.
>
> -Bill
>
> On Tue, Jul 5, 2011 at 12:50 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>
>> 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
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 05 2011 - 13:00:04 PDT
