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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jul 01 2011 - 10:00:03 PDT
