[AMBER] PDDG-PM3/MMGBSA calculation

From: Giovanni Grazioso <giovanni.grazioso.unimi.it>
Date: Fri, 14 Feb 2014 17:26:49 +0100

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.

Giovanni

-- 
*****************************************************************
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 Fri Feb 14 2014 - 08:30:03 PST