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
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Jul 05 2011 - 10:00:07 PDT
