OK, but unfortunately I still get the same error message:
PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB C8
when I run the serial program.
Holly
On Thu, May 29, 2014 at 10:44 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Perfect!
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, and
> Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Thu, May 29, 2014 at 7:34 AM, Masao Fujinaga <fujinaga.ualberta.ca>
> wrote:
> > Hello Ray,
> > The serial tests all passed.
> >
> > Masao
> >
> > On 2014-05-28, 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
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> > --
> > Masao Fujinaga
> > fujinaga.ualberta.ca
> > Research Computing Support
> > Information Services and Technology (IST)
> > University of Alberta, Edmonton, Alberta, CANADA T6G 2H1
> >
>
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>
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Received on Thu May 29 2014 - 12:00:02 PDT
