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
>
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Received on Wed May 28 2014 - 11:30:02 PDT
