ADL: mismatch between AD4 and vina resuts

Revthi Sanker revthi.sanker at
Thu Jun 20 21:00:36 PDT 2013

Dear Sir,
Thank you so much for replying to my query. That either of 
the conformations is wrong, would actually affect the very first step in
 my research. I intended to use this docked complex as the starting 
structure for performing MD simulations from where I want to predict 
crucial binding site interactions to propose mutations in the protein. 
The two poses from AD4 and vina are significantly different, I do not 
have any residues in common. How am I supposed to proceed with my 
research further? Kindly provide your valuable comments in this issue. 
Thank you in advance.

M.S. Research Scholar
Indian Institute Of Technology, Madras

 From: Oleg Trott <trott at>
To: autodock at; Revthi Sanker <revthi.sanker at> 
Sent: Friday, 21 June 2013 12:06 AM
Subject: Re: ADL: mismatch between AD4 and vina resuts

Presumably, at least one of the two results is wrong. The Vina FAQ
explains how the binding pose could end up being incorrect (and almost
all of the possibilities apply to AutoDock 4 as well).

On Thu, Jun 20, 2013 at 6:12 AM, Revthi Sanker <revthi.sanker at> wrote:
> Dear all,
> I was initially using ADT4 for protein-ligand docking and I got four clusters with the best binding energy(B.E) being -7.0. When I tried using vina, for the same grid box parameters, I obtained a B.E of -9.9 and the position was very different from my AD4 results. why is there a discrepancy between the results of AD4 and vina?how can the binding energy vary so much?
> Kindly explain me this issue.
> Thanks for your help in advance
> Revathi
> M.S. Research Scholar
> Indian Institute Of Technology, Madras
> India
> ________________________________________________
> --- ADL: AutoDock List  --- ---

Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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