Compatibility with Meeko

[KSUN63]

Hi there,

Many thanks to this super awesome project. I wonder if compatibility with Meeko was something on your mind? I tried it and Meeko seems to have a hard time converting the generated result back to the sdf format. Is this something that you plan to address at some point? Or am I missing something there?

Best,
Oliver

[rwxayheee]

Hi @KSUN63

Contributor to Meeko here. If you're attempting to convert PDBQT to SDF without using Meeko for ligand preparation, the standard Meeko pipeline might need additional information to accurately interpret the chemical structures. For guidance on generating the necessary annotations (like index maps) AFTER DOCKING, please check out this discussion:

forlilab/Meeko#305

Feel free to open a new issue in our repository https://github.com/forlilab/Meeko/issues if you might need any further assistance.