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
Received on Sat Jul 02 2011 - 17:30:04 PDT
