Issue with Docking Pipeline

[Ash100]

Hi Ryan,

The docking pipeline is failing to generate pdbqt files, although i did not see any apparent issue except python which is shifted to 3.12 on colab.

Would you be able to fix it?
Best Regards,

[RyanZR]

Hi @Ash100, thanks for the heads up.
I will be looking into it soon.

[Ash100]

Thanks Ryan, I tried fall back runtime in colab and that is working fine. The rest i tried different things but the issue seems with vina scripts, as colab is shifted to 3.11.11 in late December 2024.

[RyanZR]

While I'm not entirely sure about the issue with the failure to generate pdbqt file, I did notice that using mk_prepare_receptor.py from meeko 0.6.1 in the current docking pipeline may not able to generate protein PDBQT file. It would be better if you could reproduce the error or attach the error message along with the labodock_install.log file.

I also noticed that the package installation failed due to the recent shift to Python 3.11.11 in Colab.

In the meantime, I've updated the Python version in environment.yml file. The docking pipeline should now be working correctly.

Please try the notebooks from the develop branch and let me know if this resolves the issue.

[rwxayheee]

Hi @RyanZR
Thanks for the nice work. I wrote the notebooks for Meeko documentation:
https://meeko.readthedocs.io/en/release-doc/colab_examples.html
Would you be able to take a quick Look at my setup? Specifically, I would like to know how we can help with a workaround or setup for a specific Python environment. Currently Meeko needs Python >= 3.9 and <3.12, but there are workaround if you need it with older and newer Python. See here for a brief note on Python version

https://meeko.readthedocs.io/en/release-doc/installation.html#support-for-python-3-12

Feel free to reach out if we could be of any further assistance. Thank you for considering Meeko in your workflows