Dear Jason,
thanks for all, now also DFTB works well!
Best regards
Giovanni
Il 16/02/2014 03:13, Jason Swails ha scritto:
> 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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>
>
--
*****************************************************************
Dr. Giovanni GRAZIOSO
Senior Researcher
Università degli Studi di Milano - Scienze del Farmaco
Dipartimento di Scienze Farmaceutiche - DISFARM
Sezione Chimica Farmaceutica "Pietro Pratesi"
Via L. Mangiagalli 25 - 20133 Milano (Italy)
Phone: +039/02503-19352 - Lab: +039/02503-19351
Fax: +039/02503-19326
e-mail: giovanni.grazioso.unimi.it
Web site: http://users.unimi.it/grazioso
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Received on Tue Feb 18 2014 - 08:30:02 PST
