<p>I have an sdf file of multiple ligands which is optimized previously with rdkit. Now I want to convert it to pdbqt format suitable for docking in one go - not manually and not with obabel. However the valencies should be satisfied correctly in the output when we add hydrogens.</p>
<p>How can I do this?</p>

CC BY-SA 4.0
2024-12-13T13:10:56.230Z
What about AutoDockTools? Also what languages are you familiar with? Python because I assume thats what is meant by RDKit? Are you looking for us to write the code for you (it's a fair amount of code) or just give advice? If you want us to write the code, generally we'd ask what code have your tried. Its not a hard task BTW, its just the way we answer things.
M__
CC BY-SA 4.0
2024-12-14T13:37:44.123Z
meaning you want us to suggest a library that does that ?? try this  https://oddt.readthedocs.io/en/latest/rst/oddt.toolkits.extras.rdkit.html#oddt.toolkits.extras.rdkit.MolToPDBQTBlock  from https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/tencent_8D4F6996C36D1BC76C22068BDE1C6664ED06%40qq.com/#msg36978353
pippo1980
CC BY-SA 4.0
2024-12-14T14:28:28.697Z
We wants advice...
Dikshit Rathva
CC BY-SA 4.0
2024-12-26T15:57:50.777Z
use one of various tools sdf->pdb, then pdb->pdbqt with autodock tools.
Maximilian Press
<docking><autodock>
Conversion of multiple sdf files to pdbqt format
# Conversion of multiple sdf files to pdbqt format

(Asked by: username_0 on 2024-12-13)

I have an sdf file of multiple ligands which is optimized previously with rdkit. Now I want to convert it to pdbqt format suitable for docking in one go - not manually and not with obabel. However the valencies should be satisfied correctly in the output when we add hydrogens.

How can I do this?

**Tags:** docking, autodock
> **Comments:**
> **username_1**: What about AutoDockTools? Also what languages are you familiar with? Python because I assume thats what is meant by RDKit? Are you looking for us to write the code for you (it's a fair amount of code) or just give advice? If you want us to write the code, generally we'd ask what code have your tried. Its not a hard task BTW, its just the way we answer things.  
> **username_2**: meaning you want us to suggest a library that does that ?? try this  https://oddt.readthedocs.io/en/latest/rst/oddt.toolkits.extras.rdkit.html#oddt.toolkits.extras.rdkit.MolToPDBQTBlock  from https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/tencent_8D4F6996C36D1BC76C22068BDE1C6664ED06%40qq.com/#msg36978353  
> **username_0**: We wants advice...  
> **username_3**: use one of various tools sdf->pdb, then pdb->pdbqt with autodock tools.  

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## 0 answers

