Protein_ligand.ipynb pybel issue

[kva0987]

Hi,

I was running Protein_ligand module.

While I was running to provide input files, there was an error message saying pybel that it cannot import pybel.

Also, when I tried to "Enumerate Stereoisomers to generate ligand topology", I see error message as below;

---

AttributeError Traceback (most recent call last) in 8 ##@markdown You can find the smiles for your lingad at: https://pubchem.ncbi.nlm.nih.gov/ 9 ---> 10 mol= [m for m in pybel.readfile(filename=ligand_pdb2, format='pdb')][0] 11 mol.calccharges 12 mol.addh()

AttributeError: module 'pybel' has no attribute 'readfile'

Could you look into this issue?

Best,

[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