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-- 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed May 28 2014 - 16:30:02 PDT