Thank you very much for your reply.
No, I have commented the PB section in the script to see whether GB section
does work properly or not. I have seen GB section works well but when I
uncommented PB section then it shows the weired error. However, GB
calculation uses mmpbsa_py_energy program.
Thanks again
Sudipta
On Mon, Jul 23, 2012 at 2:03 PM, Miguel Ortiz Lombardia <
miguel.ortiz-lombardia.afmb.univ-mrs.fr> wrote:
> El 23/07/12 22:03, sudipta escribió:
> > 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
> >
>
> Hi Sudipta,
>
> It looks like in your input file the PB section is commented out (with
> '#' characters) That should explain why these calculations are not
> carried out.
>
>
> --
> Miguel
>
> Architecture et Fonction des Macromolécules Biologiques (UMR7257)
> CNRS, Aix-Marseille Université
> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
> Tel: +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
>
> _______________________________________________
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>
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Received on Mon Jul 23 2012 - 14:30:07 PDT
