ADL: AutoDock Vina with Flex residues!

Wim Nerinckx wimnerinckx at
Fri Apr 24 11:07:00 PDT 2009

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.
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
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