ADL: Binding affinity contributions

#SK MAHASIN ALAM# SKMA0001 at e.ntu.edu.sg
Fri Jun 28 00:08:16 PDT 2013


Dear Friends,



I am performing docking study of Cu-complex with G-quadruplex using Autodock Vina. For one of my lignads the calculated binding affinity is -7.5 kcal/mol.



(a Is it possible to know the contribulations of hydrophobic, hydrogen bonding etc to the calculated binding affinity in terms of energy, e.g., how much kcal/mol is contributed to -7.5 kcal/mol due to hydrogen bonding?



(b) what is the physical meaning of gauss1 and gauss2?



(c) Is Vina program considered the electrostatic interactions?



Thanks a lot for your kind helps and valuable time.



Warm regards



Mahasin


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