ADL: mismatch between AD4 and vina resuts

Revthi Sanker revthi.sanker at
Sat Jun 22 03:38:03 PDT 2013

Dear Sir,
My grid space is 24*28*28 and the I have used the same dimensions and box center in both the cases. Performing MD on both becomes a must but i am afraid as the two positions are entirely different it will significantly affect the mechanism that I am trying to hypothesize. And yes,,there is not a single residue that is common to the two sites I got from AD4 and vina.
Thank you in advance for your suggestions.
 M.S. Research Scholar
 Indian Institute Of Technology, Madras

 From: Douglas Houston <DouglasR.Houston at>
To: autodock at 
Sent: Friday, 21 June 2013 3:12 PM
Subject: Re: ADL: mismatch between AD4 and vina resuts

You could perform MD on both - the list of residues to mutate would be  
longer but perhaps still practical. Although it's odd there are no  
residues at all in common. Are you sure your search space is small  
Quoting Revthi Sanker <revthi.sanker at> on Fri, 21 Jun 2013  
12:00:36 +0800 (SGT):

> 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.
> ​Revathi.S
> 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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Dr. Douglas R. Houston
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