ADL: mismatch between AD4 and vina resuts

Oleg Trott trott at scripps.edu
Thu Jun 20 11:36:58 PDT 2013


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 yahoo.com> 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
> ________________________________________________
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com



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