# Error when running molecular docking

**URL:** <https://help.galaxyproject.org/t/error-when-running-molecular-docking/16409>\
**Category:** usegalaxy.org support\
**Tags:** tool-help\
**Created:** [October 20, 2025, 11:09am UTC](https://help.galaxyproject.org/t/error-when-running-molecular-docking/16409 "2025-10-20T11:09:22Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 21, 2025, 12:27am UTC](https://help.galaxyproject.org/t/error-when-running-molecular-docking/16409/2 "2025-10-21T00:27:04Z")

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Welcome @Jeslyn_Jaic

I just replied to another question about an error with this same tool. Was this also yours? [Empty Output folder - Vina Docking](https://help.galaxyproject.org/t/empty-output-folder-vina-docking/16410)

If not, maybe the content helps. Meanwhile, I am generating an example history from our tutorial and will post that back next. I’ll be using the data and workflow from here. My test will confirm that the tools are working as expected.

- [Hands-on: Protein-ligand docking / Protein-ligand docking / Computational chemistry](https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html)

You could also try to see how the processing flows through the tool but maybe more importantly for your use case, examining the content of the files seems more important.

Why? You messages are about the **content of your ligand inputs**.

> [@Jeslyn\_Jaic](#):
>
> ```auto
> PDBQT parsing error: Unknown or inappropriate tag found in flex residue or ligand.
> > ROOT
> 
> ```

* * *

What happens if you split up the multi-ligand SDF first, then run the collection of PDBQT files through this tool? Something like this:

> [@Empty Output folder - Vina Docking](https://help.galaxyproject.org/t/empty-output-folder-vina-docking/16410/4):
>
> - Prepare your inputs with **Prepare ligands for docking** OR **Prepare ligand**
> - Input the PDBQT collection to **VINA Docking**
> - Each ligand will have a separate job, and those outputs will be written to a collection.

More soon as a process the tutorial. Once you have results from the splitting, you can also post back. Sharing the history is an easier way to offer feedback and involves just a single link. You can unshare after we are done. → [How to get faster help with your question](https://help.galaxyproject.org/t/how-to-get-faster-help-with-your-question/11469)

Let’s start there, thanks! 🙂

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