Does it work if you only do one snapshot? Don't forget to remove the files
that mm_pbsa.pl writes if you restart a simulation, since
mm_pbsa.pltypically appends to files, and you don't want it to append
to files that
begin with a failed calculation. This should help you pinpoint the problem
-- it could be that the prmtop files are incompatible with the trajectories,
certain residues were improperly specified, etc.
Hope this helps,
Jason
On Tue, Sep 14, 2010 at 10:55 PM, manoj singh <mks.amber.gmail.com> wrote:
> Thanks for the reply,
>
> Yes! I applied all bugfixes. This is Amber10.
>
> --
>
> On Tue, Sep 14, 2010 at 10:52 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Have you applied all bugfixes? What version of amber are you using?
> >
> > On Tue, Sep 14, 2010 at 9:59 PM, manoj singh <mks.amber.gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > I am using mm_pbsa.pl to do per-residue decomposition. The calculation
> > > appears to be trapped in a infinite loop with the following message. I
> > have
> > > no clue what is going on and will be very thankful for any response.
> > >
> > > Manoj
> > >
> > > -----
> > >
> > > No values for GB_TGBSUR existing -> Skipping
> > > Processing PB SPBSOL
> > > Doing 1 PB SPB
> > > Doing 1 GB SGBSUR
> > > No values for GB_SGBSUR existing -> Skipping
> > > Processing PB TPBTOT
> > > Doing 1 PB TPBSOL
> > > No values for PB_TPBSOL existing -> Skipping
> > > Processing PB BPBTOT
> > > Doing 1 PB BPBSOL
> > > No values for PB_BPBSOL existing -> Skipping
> > > Processing PB BPBSOL
> > > Doing 1 PB BPB
> > > Doing 1 GB BGBSUR
> > > No values for GB_BGBSUR existing -> Skipping
> > > Processing PB SPBTOT
> > > Doing 1 PB SPBSOL
> > > No values for PB_SPBSOL existing -> Skipping
> > > Processing PB TPBSOL
> > > Doing 1 PB TPB
> > > Doing 1 GB TGBSUR
> > > No values for GB_TGBSUR existing -> Skipping
> > > Processing PB SPBSOL
> > > Doing 1 PB SPB
> > > Doing 1 GB SGBSUR
> > > No values for GB_SGBSUR existing -> Skipping
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Sep 14 2010 - 20:30:03 PDT
