converting pdbqt files to sdf when not prepared with Meeko

[TommyBiomodellingAU]

hello vina devs
how do I safely convert pdbqt files to sdf when not prepared with Meeko? obabel can technically do it, but is generally regarded as an unsafe method to do so, no?

[diogomart]

Hello,
Yes, see https://github.com/forlilab/Meeko?tab=readme-ov-file#2-convert-docking-results-to-sdf

[rwxayheee]

Hi @TommyBiomodellingAU

See a recent post in Meeko, in case you are still interested in processing PDBQT files (into RDKit molecules) not initially annotated by Meeko:
forlilab/Meeko#305 (comment)
In this discussion, we demonstrate a way to reconstruct atom index mapping and hydrogen-parent mapping given a Smiles string.

Closing as resolved.