Thanks
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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Received on Sat Feb 15 2014 - 12:00:02 PST
