HI Ray,
My system contain a protein-DNA complex. But the protein is a zinc finger
protein and I have modeled ZN atom as a nonstandard residue. So, what shall
I do next?
Thanks
Sudipta
On Mon, Jul 23, 2012 at 2:54 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> 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
> > > >
> > > > _______________________________________________
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> > > >
> > > >
> > >
> > >
> > > --
> > > 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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> >
> >
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Received on Mon Jul 23 2012 - 15:30:03 PDT
