ADL: help virtual screening

Wim Nerinckx wimnerinckx at
Wed Jun 3 15:47:04 PDT 2009

Hi Venkat,

Here is a possibility:

The AutoDock VS tutorial files contains the python script  
"" that is undocumented in the manual  
UsingAutoDock4forVirtualScreening_v4.pdf. You can use it with e.g.

/ -i yourmultimolfile.mol2

That will split the "yourmultimolfile.mol2" into single mol2 files,  
one per molecule. Thereafter you can use the documented script for  
converting them all into pdbqt files.

But I guess it is possible to do both together with a single script...


On 04 Jun 2009, at 00:36, venkat wrote:

> Hi all
> I would like to do virtual screening using autodock / vina.
> I do download the mol2 file from database, which has more than  
> 1000, compounds.
> Spliting all the file to single mol2 and do the pdbqt for docking  
> really time consuming.
> Is it any script or command line program that could generate pdbqs  
> for all the mol2 file ?
> Or let  me know is ther any efficient way to handle huge database  
> without going through single
> pdb for create the input (pdbqs) for docking.
> Really appreciate if any one could give some suggestions or any  
> program they could able to share.
> thanks
> venkat
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