Ray,
Did you run my files at all to see if it is just a compilation problem that
we have?
Thanks,
Holly
On Wed, May 28, 2014 at 5:23 PM, Hallel Freedman <hfreedma.ualberta.ca>wrote:
> 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
>> >>> > _______________________________________________
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>> >>> > AMBER.ambermd.org
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>> >>>
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>> >>
>> >>
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Received on Wed May 28 2014 - 20:00:02 PDT
