ADL: AutoDock Vina with Flex residues!

Oleg Trott trott at scripps.edu
Mon Apr 27 14:02:50 PDT 2009


Wim,

The paper has been accepted, so it shouldn't be long now.

Regarding NCI Diversity2, I can send you the PDBQT files, but I'm
hoping to get some feedback regarding its quality (i.e. any kind of
mistakes) from such early testers, before we put it up on the web.

Cheers,
Oleg

On Fri, Apr 24, 2009 at 11:07 AM, Wim Nerinckx <wimnerinckx at lavabit.com> wrote:
> Hi Warren,
> The procedure for flexible residue preparation is the same as in AutoDock4!
> Just prepare the 2 pdbqt files with ADT as in the AutoDock4 manual. Find
> underneath a simple conf.txt example for Vina.
> I find that Vina (last version on a Mac) does it remarkably well with
> glycoside hydrolases, even when docking tetrasaccharide-analogs. Oleg truly
> made a breakthrough here. Let's hope that their paper is soon on-line. And
> that the Scripps group releases a diversity set that is all-ready as pdbqt
> so that we can set our processors in the red zone by virtual screening with
> Vina.
> Greetings,
> Wim, Belgium
>
>
>
> ******************
>
> receptor = your_receptor_noflex.pdbqt
> flex = your_flexes.pdbqt
> ligand = your_ligand.pdbqt
>
> all = all.pdbqt
>
> center_x = 2.9
> center_y = -7.1
> center_z = 0.8
>
> size_x = 12
> size_y = 18
> size_z = 12
>
> exhaustiveness = 8
> energy_range = 3
>
> *************************
>
> On 24 Apr 2009, at 19:04, Warren Menezes wrote:
>
>> Dear Friends,
>> I have now performed several dockings using the latest version of AutoDock
>> Vina (Great Program!!), in which the active receptor site is set as rigid.
>>  I would like to prepare a pdpqt file with flexible residues.  I have
>> identified the residues to flex, but I would like to know the procedure to
>> prepare the input flex-residues file using any program such as,  ADT, Pymol,
>> or even MS Word, Thanks!
>>
>> With Best Regards
>> Warren
>> Chicago
>> USA
>>
>> ________________________________________________
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>
>
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>



-- 
Oleg Trott, Ph.D. (Columbia University)

http://olegtrott.com



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