Analyze Autodock Vina poses.

[Le-Phung-Hien]

Hi team,

Thanks for the great tool.

I am trying to streamline my docking analysis. AutoDock Vina results has two pdbqt file, one for different poses of the ligand, and one for the protein. Just want to ask if ProLIF can identify and virtualize the receptor-ligand interactions with pdbqt files, or I need to convert the ligands to pdb or sdf file?

Thanks!

[cbouy]

Hi,

Please refer to the docking section of the tutorials. Short answer:

• for the protein you'll need a non-PDBQT file (most likely a PDB file) with explicit hydrogens
• for the ligand poses, you can use:
  • the prolif.pdbqt_supplier(pdbqt_files, template) function where pdbqt_files is a list of paths to each individual pose PDBQT file (which you can obtain with the vina_split command), and template is an RDKit mol with the correct bond orders and charges (since PDBQT format lacks those).
  • alternatively, you can convert your PDBQT files to an SDF, I think meeko does this pretty well (don't use openbabel) and then use prolif.sdf_supplier

Please close this issue if this answers your question!

[Le-Phung-Hien]

Thank you very much!