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
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Received on Tue Jul 05 2011 - 15:30:03 PDT
