ADL: mismatch between AD4 and vina resuts

Oleg Trott trott at scripps.edu
Tue Jun 25 14:41:44 PDT 2013


I'd like to clarify that while Vina does use Angstroms to measure
distances, the internal grid spacing is not 1 Angstrom (which would
probably be bad). Moreover, for local searches and refinements at the
end of docking, grids aren't even used.

On Sat, Jun 22, 2013 at 7:13 AM, Parker de Waal
<Parker.deWaal09 at kzoo.edu> wrote:
> 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
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
> ________________________________________________
> --- 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


More information about the autodock mailing list