ADL: help virtual screening

venkat vkabas at
Wed Jun 3 20:30:48 PDT 2009

Thanks Wim.

But still waiting there is any potential way to do pdbqt files.

i did able to split the mol2 by split command.

Hoping there are some experts have all in one script file or some other easy way to do this !!!!!?

Do you have that python script that you could send me,


----- Original Message ----
From: Wim Nerinckx <wimnerinckx at>
To: autodock at
Sent: Wednesday, June 3, 2009 6:47:04 PM
Subject: Re: ADL: help virtual screening

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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