Hi Ray,
Thank you very much for explaining this. I will try again and see what
happens.
Best regards,
Holly
On Thu, May 29, 2014 at 4:53 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Looks like you are using radiopt = 1, i.e. asking pbsa to assign
> radius for that atom CB/C8. Please use radiopt=0. Of course if you use
> the latest AmberTools, this should have been fixed, i.e. radipot=0 by
> default.
>
> Nonpolar solvents (inp=1 or inp=2) should not have any of this
> problem, again if you are using the latest AmberTools.
>
> 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 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
> >> >
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > AMBER mailing list
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>
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Received on Thu May 29 2014 - 17:30:02 PDT
