On Sat, Feb 15, 2014 at 2:49 PM, Giovanni Grazioso <
giovanni.grazioso.unimi.it> wrote:
> Thanks
>
Try recompiling now. The update should be available. Let me know if this
doesn't work. (Note, after recompiling you should be able to use the
command "MMPBSA.py -rewrite-output" to avoid rerunning the calculation).
Thanks!
Jason
>
>
> GG
>
> Jason Swails <jason.swails.gmail.com> ha scritto:
>
> >On Sat, Feb 15, 2014 at 11:13 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >>
> >>
> >>
> >> On Fri, Feb 14, 2014 at 11:26 AM, Giovanni Grazioso <
> >> giovanni.grazioso.unimi.it> wrote:
> >>
> >>> Hi,
> >>>
> >>> I want to calculate the free energy of binding of a ligand into the
> >>> binding cleft of a protein by QM-MMGBSA approach and MMPBSA.py.
> >>>
> >>> By PM3 and AM1 hamiltonians all the results were correctly obtained but
> >>> if I wanted to use PDDG-PM3 methods I had this error:
> >>>
> >>> /Beginning GB calculations with ...//
> >>> // calculating complex contribution...//
> >>> // calculating receptor contribution...//
> >>> // calculating ligand contribution...//
> >>> //IndexError: list index out of range//
> >>> //Exiting. All files have been retained//
> >>> /
> >>>
> >>> No errors were found in the temporary files. I suppose that the problem
> >>> could be in the final scripts able to capture the energy values from
> >>> _MMPBSA_* files.
> >>>
> >>> Thanks in advance for help.
> >>>
> >>
> >> I've received a similar report recently that is likely a result of an
> >> issue with MMPBSA.py. I am looking into it and will hopefully have a
> fix
> >> shortly.
> >>
> >
> >I've found the problem and fixed it. I will create a bugfix for it
> >hopefully before the end of the weekend.
> >
> >All the best,
> >Jason
> >
> >--
> >Jason M. Swails
> >BioMaPS,
> >Rutgers University
> >Postdoctoral Researcher
> >_______________________________________________
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Feb 15 2014 - 18:30:02 PST
