I would suggest upgrading to AmberTools 1.5 and trying MMPBSA.py from that
package (they give compatible results for the same settings). Even if you
stay with the perl version the PBSA solver will still be updated so you may
get rid of this issue (although the numerical results will be ever so
slightly different).
HTH,
Jason
On Tue, Aug 30, 2011 at 8:07 AM, <sribone.fcq.unc.edu.ar> wrote:
> Dear Neha, you have the answer in the amberlist:
>
> http://archive.ambermd.org/200407/0279.html
>
> Regards,
>
> > Dear list,
> >
> >
> > I am running MM-PBSA using perl script in AMBER11. The job halted after
> > generating snapshots. At first I thought, it might be the improper
> numbering
> > with coordinates, but I verified the coordinates. I get following
> message.
> >
> >
> --------------------------------------------------------------------------------
> > 4. RESULTS
> >
> --------------------------------------------------------------------------------
> >
> > PB bomb in pb_reslist(): maxnbr too small
> >
> >
> > Your help is appreciated.
> > --
> > Regards,
> > Neha Gandhi,
> > School of Biomedical Sciences,
> > Curtin University of Technology,
> > GPO Box U1987 Perth,
> > Western Australia 6845
> > Phone: 9266 9061
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
> _______________________________________________
> 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
Received on Tue Aug 30 2011 - 08:00:05 PDT
