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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Received on Sat Feb 15 2014 - 09:30:02 PST
