First of all you change sdf to pdb from discovery studio and then pdb file change into pdbqt by autodock4 tool.

Dear Thiago Alcantara

There is numerous way to convert all the files into .pdbqt but You simply can use open babel or just import your ligands into autodock and then export (save as) into pdbqt.

@Waseem Ahmad Ansari, Shaban Ahmad

Thanks, but in autodock it can't open lots of sdf at once.

The simple way to do that is what waseem recommend.

£I have same problem , i draw molecule and i saved forma sdp . second step i can not exploited

how can i used autodock vina to get pdbQT (autodock vina installed but icone doesnt exixte in desktop)

You can use PyRx software for converting SDF to pdbqt

you can convert it via chimera app

Addadi Khadidja

Hello

Autodock Vina does not show icon its script works by command terminal you input the command and run. That's it

Use OpenBabel software

How can we do using open babel with a set of commands because the number of ligands is multiple about 500

This might help:

https://www.youtube.com/watch?v=uobRSy5p1ZU&t=182s

https://www.youtube.com/watch?v=uobRSy5p1ZU&t=236s

This might be helpful.

you can use as they suggested pyrx or there is another alternative that is easydockvina the detail is that in some occasions these software export an erroneous format of the pdbqt and at the moment of making the calculation you can obtain erroneous results, for that reason my suggestion is before making the calculation you must check that the structures in pdbqt are correct.

You can use OpenBabel for that (the command line version) and check it documentation at https://openbabel.org/docs/dev/Command-line_tools/babel.html

obabel *.mol2 -O *.pdbqt

I suggest using the following commands in the terminal where you browse and your file to be converted should be:

1.obminimize -ff MMFF94 -n 1000 namefile.sdf

2. obabel -isdf namefile.sdf -omol2 -O namefile.mol2 -p 7.4 -m --gen3d

3. obabel *.mol2 -O *.pdbqt -m

I suggest doing it in linux, it is more user friendly.

Hi, a Python package named Meeko is designed for preparing multiple ligands for docking.

Here is a tutorial:

https://www.blopig.com/blog/2022/08/meeko-docking-straight-from-smiles-string/#:~:text=The%20protonated%2C%203D%20RDKit%20type%20molecule%20is%20converted,meeko.MoleculePreparation%20%28%29%20meeko_prep.prepare%20%28protonated_lig%29%20lig_pdbqt%20%3D%20meeko_prep.write_pdbqt_string%20%28%29

Here is Meeko git repo:

https://github.com/forlilab/Meeko

Open Babel is not recommended for converting formats. Here is why (in Chinese):

https://zhuanlan.zhihu.com/p/449740716