You are using radiopt=1 for the inp=2 option of nonpolar solvation free
energy calculation. Do you have any ligand or other nonstandard residues in
the system?
All the best,
Ray
On Mon, Jul 23, 2012 at 2:38 PM, sudipta <sudipta.mml.gmail.com> wrote:
> Hi Jason,
>
> Thank you very much for your reply.
>
> Please find the attached file. This file contains all _MMPBSA_*_pb.mdout
> files. Feel free to contact me if you need any further information from my
> side.
>
> Thanks again
> Sudipta
>
> On Mon, Jul 23, 2012 at 2:32 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hi Sudipta,
> >
> > This error message means that the PB energy calculation failed, which is
> > actually an error within PBSA. It would be more helpful to include the
> > _MMPBSA_*_pb.mdout files, since any error messages may be hidden inside
> > there.
> >
> > All the best,
> > Jason
> >
> > On Mon, Jul 23, 2012 at 4:03 PM, sudipta <sudipta.mml.gmail.com> wrote:
> >
> > > Hi Jason and Amber users,
> > >
> > > I have been facing a strange problem with PB calculation for a
> > protein-DNA
> > > system from the last week. The error looks like
> > >
> > > /home/sudipta/Downloads/amber12/bin/mmpbsa_py_energy failed with
> prmtop
> > >
> > > The script, MMPBSA.py.MPI has finished GB calculation for my system
> > without
> > > any error. Moreover, the tutorial files finish without any error.
> Please
> > > find the attached two final output files of those two calculations. It
> > > really puzzles me why PB calculation is not finishing properly for my
> > > system. I don't get any fruitful error message except the above one. By
> > the
> > > way, I am using only AmberTools12 and the OS is Ubuntu 10.4.
> > >
> > > Looking forward to hear from you soon.
> > >
> > > Thanks in advance
> > > Sudipta
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Mon Jul 23 2012 - 15:00:04 PDT
