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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 11:34 AM, Hallel Freedman <hfreedma.ualberta.ca> wrote: > 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 >> > >> >> _______________________________________________ >> 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/amberReceived on Thu May 29 2014 - 16:00:02 PDT