ADL: mismatch between AD4 and vina resuts

Parker de Waal Parker.deWaal09 at kzoo.edu
Sat Jun 22 07:13:58 PDT 2013


Is it possible that the box dimensions were generated at an improper
spacing interval?

Using AutoDockTools for AutoDock4, the grid spacing is set to a default of
0.375 Angstroms, however AutoDock Vina requires a grid spacing of 1.0
Angstroms. If you did not specify the correct spacing than your box will be
significantly larger than expected which may be the reason you are
experiencing a lack of binding overlap.

Best,
Parker


On Sat, Jun 22, 2013 at 6:38 AM, Revthi Sanker <revthi.sanker at yahoo.com>wrote:

> 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.
>  Revathi.S
>  M.S. Research Scholar
>  Indian Institute Of Technology, Madras
>
>
>
>
> ________________________________
>  From: Douglas Houston <DouglasR.Houston at ed.ac.uk>
> To: autodock at scripps.edu
> 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
> enough
> Quoting Revthi Sanker <revthi.sanker at yahoo.com> 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 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
> >> Revathi
> >> M.S. Research Scholar
> >> Indian Institute Of Technology, Madras
> >> India
> >> ________________________________________________
> >> --- 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
> >
> > http://olegtrott.com
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Room 3.23
> Institute of Structural and Molecular Biology
> Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
>
> --
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> Scotland, with registration number SC005336.
>
>
> ________________________________________________
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