Sudipta,
If you have modeled any nonstandard residue, please use radipt=0 only. This
limits your choice of nonpolar solvation treatment to inp=1 only, i.e. the
simple SA approach. We will revisit this issue in the next release to allow
people use inp=2 with nonstandard residues whether PB is requested or not.
All the best,
Ray
On Mon, Jul 23, 2012 at 3:01 PM, sudipta <sudipta.mml.gmail.com> wrote:
> 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
> > > > >
> > > > > _______________________________________________
> > > > > 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
> > > >
> > >
> > > _______________________________________________
> > > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 23 2012 - 15:30:03 PDT
