Protein_ligand.ipynb pybel issue

[pablo-arantes]

Protein_ligand.ipynb pybel issue

[kva0987]

My issue I think is similar to zjl894150094.

[kva0987]

The issue with pybel gets resolved when I do as below;

!conda install -c conda-forge openbabel
from openbabel import pybel

I think openbabel was not installed correctly.

[pablo-arantes]

Hi @kva0987,

Thank you for letting me know about the issue. I will check and back to you.

Best,

Pablo

[kva0987]

Hi,

Is it possible in Protein_ligand.ipynb, PDBFixer ligand without adding ligand hydrogens?

I am using a ligand with known protonation state, so that I want to keep the hydrogens.
But if I don't add hydrogens, chiralCentres are not defined when doing "Enumerate Stereoisomers to generate ligand topology:".

[pablo-arantes]

HI @kva0987,

I've fixed the error. Please, try again and let me know if everything is working fine.

Thank you.

Best,

Pablo