Hi
Bondi radii are essential for GB calculations, which is why you are getting
that error.
Also, as per what prof Case suggests, It is worthwhile to upgrade to
AMBERTools20 (free) and calculated MMGBSA using this version.
On Monday, May 11, 2020, MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
wrote:
> Hi Elvis,
>
> I don't define the bondi radii...I think that never I had defined
> before when I had launched this calculation, and this error didn't
> appeared...
> What do bondi raddi indicate?
>
> Thanks in advance,
>
>
> Myriam
>
> Elvis Martis <elvis_bcp.elvismartis.in> escribió:
>
> > Hi
> > Did define the bondi radii set?
> > Best Regards
> > ElMa
> >
> >
> >
> > On Mon, 11 May 2020 at 15:45, MYRIAN TORRES RICO <
> myriam.torres.iiq.csic.es>
> > wrote:
> >
> >> Hi everyone,
> >>
> >> I want to calculate GB and PB energies, but this error appears:
> >> CalcError: /opt/amber12/bin/sander failed with prmtop
> >> smp-198ptn-dry.prmtop!
> >>
> >> This is mmpbsa.in:
> >>
> >> Input file for running PB and GB
> >> &general
> >> endframe=500, keep_files=2,
> >> use_sander=1, netcdf = 1
> >> /
> >> &gb
> >> igb=2, saltcon=0.100,
> >> /
> >> &pb
> >> istrng=0.100,
> >> /
> >>
> >> any idea?
> >>
> >>
> >> Thanks in advance!
> >>
> >>
> >> Myriam
> >>
> >>
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--
Best Regards
Elvis Martis
Mumbai.
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Received on Mon May 11 2020 - 06:00:04 PDT
