Hi Ray,
I tried that, but I get the same errors.
Holly
On Wed, May 28, 2014 at 5:22 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Let's try to get it work without mpi first ...
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, and
> Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Wed, May 28, 2014 at 11:54 AM, Hallel Freedman <hfreedma.ualberta.ca>
> wrote:
> > Masao did some more work on this and found that if he first loads python
> > using
> >
> > module load application/python/2.7.3
> >
> > then the error for 04, 07, and 10 becomes
> >
> > mpirun noticed that the job aborted, but has no info as to the process
> > that caused that situation.
> >
> >
> >
> >
> >
> >
> > On Wed, May 28, 2014 at 12:13 PM, Hallel Freedman <hfreedma.ualberta.ca
> >wrote:
> >
> >> Hi Ray,
> >> Actually we got these compile errors when we tried to run the tests. I
> am
> >> also cc'ing Masao Fujinaga who compiled this for me. Can you please
> make a
> >> suggestion about how to fix this?
> >> Thanks,
> >> Holly
> >>
> >> 01_Generalized_Born:
> >> OSError: [Errno 2] No such file or directory:
> >> '_MMPBSA_complex_gb_surf.dat.0'
> >>
> >> 02_Poisson_Boltzmann:
> >> IOError: Input file (_MMPBSA_pb.mdin) doesn't exist
> >>
> >> 04_Per_Residue_Decomp:
> >> CalcError: /lustre/jasper/software-build/amber/amber12/bin/sander failed
> >> with prmtop ../EstRAL_Files/rec.top!
> >>
> >> 07_Comprehensive:
> >> ValueError: invalid literal for float(): PB NB li
> >>
> >> 08_Stability:
> >> mpirun noticed that the job aborted, but has no info as to the process
> >> that caused that situation.
> >>
> >> 10_QM_MMGBSA:
> >> CalcError: /lustre/jasper/software-build/amber/amber12/bin/sander failed
> >> with prmtop ../EstRAL_Files/lig.top!
> >>
> >>
> >> On Tue, May 27, 2014 at 1:41 PM, Ray Luo, Ph.D. <ray.luo.uci.edu>
> wrote:
> >>
> >>> Please share with us your input file … Make sure you have patched all
> >>> updates and passed the tests.
> >>>
> >>> Ray
> >>> --
> >>> Ray Luo, Ph.D.
> >>> Professor,
> >>> Biochemistry, Molecular Biophysics, and
> >>> Biomedical Engineering
> >>> University of California, Irvine, CA 92697-3900
> >>>
> >>>
> >>> On Tue, May 27, 2014 at 11:05 AM, Hallel Freedman <
> hfreedma.ualberta.ca>
> >>> wrote:
> >>> > Dear AMBER helplist,
> >>> > I have been trying to use MMPBSA and I keep getting this error:
> >>> >
> >>> > CalcError: /global/software/amber/amber13/bin/mmpbsa_py_energy failed
> >>> with
> >>> > prmto
> >>> > p ../leapdir/complex.top!
> >>> > PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB
> C8
> >>> >
> >>> > I know that there has been discussion on similar problems in the
> past,
> >>> but
> >>> > it was hard for me to understand for mreading these what the best
> fix is
> >>> > for this problem.
> >>> > I used the ff12SB force field to create my topology files.
> >>> > Thanks,
> >>> > Holly
> >>> > _______________________________________________
> >>> > AMBER mailing list
> >>> > AMBER.ambermd.org
> >>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
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> >>>
> >>
> >>
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Received on Wed May 28 2014 - 16:30:02 PDT
