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.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Feb 15 2014 - 08:30:03 PST
