Hi Bill,
Yes, I've downloaded the bugfix.all at "
http://ambermd.org/bugfixesat.html" for version 1.5 and patched the source codes before compiling them. If you could tell me which bug particularly you are looking for, I can manually check it again.
Thanks
Ye
On Jul 5, 2011, at 5:14 PM, Bill Miller III wrote:
> Have you applied all the AmberTools 1.5 bugfixes? This was a bug that I
> found in the code a while back, and I thought it had been added to the known
> patches.
>
> -Bill
>
> On Tue, Jul 5, 2011 at 3:53 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>
>> 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
>>>
>>
>>
>> _______________________________________________
>> 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 Wed Jul 06 2011 - 08:00:05 PDT
