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
>>
>
>
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Received on Wed May 28 2014 - 12:00:04 PDT
