Protein-ligand docking error

I have been trying to following this tutorial for protein-ligand docking(Protein-ligand docking). I used 200 coumarin derivatives as my ligand library which I got in pdf format from MolPort. However, the vina docking step produces an error. I have followed all the steps carefully, I’m not sure what the mistake could be. Any help is appreciated. Thanks

Hi @Vibha_Rao

PDF and PDBQT are two different formats but maybe that was a typo?

Does the tutorial data work?

One key tip when troubleshooting data → Consider loading the tutorial data, and the tutorial workflow, and running that to create a sort of “reference history” to learn the steps and expected data formats.

That said, we recently updated some of the tools at, and are adjusting the allocated resources. If you cannot solve the problem, and the tutorial data also fails, I would be interested in reviewing since we haven’t had much reported for the proteomics tools yet.

Please send in a bug report directly from the red error dataset to the server admins at and copy/paste the URL link to this topic in the comments, along with anything else you think would be helpful for us when reviewing. Leave all data undeleted please. How-to Troubleshooting errors

Thanks in advance for the followup :slight_smile:

Hi, thank you for your response.
I meant to type sdf, not pdf.
Here is a link to my history that might help review the error.

Hello @Vibha_Rao

Ok – I took a closer look.

Technically, tools in that tutorial are not supported at any public Galaxy server but there is a Docker image available that you could try. At the top of tutorials, check the “Available at these Galaxies” to learn this next time.

For you work so far, it seems the problem was introduced when generating the ligands. Expand the dataset to see the warnings in the “info” field. Maybe the options used are not a fit for the data?