ADL: AutoDock Vina: New Question(s)

Sargis Dallakyan sargis at scripps.edu
Mon Apr 13 13:57:11 PDT 2009


Warren Menezes wrote:
> ** 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.

Hi Warren,

Thanks you for the message. Electrostatic energy by itself has no 
physical meaning and only the energy difference computed in some cycle 
can be measured:

http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_calculate_a_binding_energy%3F
http://www.ncbi.nlm.nih.gov/pubmed/17964951

> (ii) I am not an expert with ADT, so I was wondering if 'APBS' refers to some type of force field (AMBER, CHARM, etc).

APBS uses pqr input files and I've included pdb2pqr with MGLTools that 
supports AMBER, CHARMM and PARSE force fields. Use 'Compute' -> 
'Electrostatics' -> 'Preferences' to modify pdb2pqr preferences. One can 
also use pqr generated with the latest version of pdb2pqr that has 
additional options and new force fields:

http://pdb2pqr-1.wustl.edu/pdb2pqr


Thank you for using our tools,
Sargis

-- 

Sargis Dallakyan, Ph.D. - Research Programmer III
The Scripps Research Institute,
Dept. Molecular Biology,  MB-5,
10550  North Torrey Pines Road,
La Jolla,  CA 92037-1000
Tel: (858) 784-9559
http://mgltools.scripps.edu/Members/sargis


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