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-- 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 > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu May 29 2014 - 10:00:02 PDT