ADL: mismatch between AD4 and vina resuts
revthi.sanker at yahoo.com
Thu Jun 20 21:00:36 PDT 2013
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 scripps.edu>
To: autodock at scripps.edu; Revthi Sanker <revthi.sanker at yahoo.com>
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 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
> M.S. Research Scholar
> Indian Institute Of Technology, Madras
> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
Oleg Trott, Ph.D. (Columbia University)
Staff Scientist in the Olson Lab
The Scripps Research Institute
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