ADL: AutoDock Vina with Flex residues!

Wim Nerinckx wimnerinckx at
Fri Apr 24 12:35:16 PDT 2009

Hi Warren,

You must make two "special" pdbqt files: one of your receptor that is  
missing the residues that will be flexible, and one that contains the  
flexible residues (and also contains info on what of them that you  
wish to be flexible). It is very well explained (better than I  
possibly can) in the AutoDock4 - ADT manual, so I suggest that you  
first exactly repeat the example for making those two pdbqt-files  
(with the program ADT) as described in that manual (without actually  
doing the docking but you may try Vina here and it will work!) and  
thereafter you're set to do the same with your own receptor and  
ligand. It is somewhat weird at first but it is actually relatively  
simple. What is very-very nice is that the "all.pdbqt" file, that  
Vina generates when doing a flexible docking, will also contain the  
reoriented flexible residues (yes, per docked result, very well  
done!!), and you can open it with Pymol and skip through the results  
just like Oleg described it in his vdeo tutorial.

Congrats, Oleg!

Ghent University, Belgium

On 24 Apr 2009, at 20:56, Warren Menezes wrote:

> Hi! Wim,
> The problem is that I have never used Autodock4 (or any of the  
> previous versions).  I went directly from ADT to Autodock Vina,  
> Thanks to Oleg's video tutorial.  I understand the conf.txt file  
> you posted, but my problem is with the preparation of  
> "your_flexes.pdbqt" file?  What editor/program to use to prepare  
> this file, Thanks!
> Warren
> Chicago

More information about the autodock mailing list