ADL: AutoDock Vina: New Question(s)

Warren Menezes wmenezes at
Mon Apr 13 13:15:58 PDT 2009

** High Priority **

Dear Friends,
I have been using Autodock Vina for the past 2 months (in fact I bypassed Autodock 4.0 and picked up my docking tools of trade from the excellent Vina tutorial).  Recently, I blind-docked a drug-ligand onto a receptor protein using the latest Autodock Vina 1.0 beta 04.  It's sure fast!  I obtain a reasonable number, - 6.3 kcal/mol for the binding affinity of the ligand.  I wanted to calculate the total energy of the docked protein, so I turned to ADT and used the command 'Compute Potential Using APBS', which is under the menu command 'Compute' and then select 'Electrostatics'.  I got a value of 4.4716E4 kJ/mol.  I repeated the same calculation on the protein without the docked ligand and I got 4.4525E4 kJ/mol for the potential.  Since I am new to ADT, I would like you advice/comment regarding the following:
(i) the numbers imply that overall the docked protein is unstable by about 200 kJ/mol relative to the undocked protein.  Therefore, even though the ligand binds favorable to the active site on the protein (thus locally stabilizing the active site), overall the docking destabilizes the protein, which in turn responds by sending the next signal.
(ii) I am not an expert with ADT, so I was wondering if 'APBS' refers to some type of force field (AMBER, CHARM, etc).
With Best Regards
Chicago, USA

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