Custom ligand conformer issues

[AlvinAi-cloud]

When a custom ligand is provided from PDB, it creates conformer generation issues.
Is there a way to provide conformers? Or the ligand can be provided in other formats (e.g., SMILE, SDF)?

15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.io.tools.rdkit: Encountered BondType.ANY. Interpreting as single bond.
15:39:07 WARNING atomworks.ml.transforms.rdkit_utils: Initial conformer generation based on distance geometry failed. Successful: 0. Falling back to generating a conformer starting from random coordinates.
15:39:09 WARNING atomworks.ml.transforms.rdkit_utils: Failed to generate 1 conformers for UNL. Falling back to zeros.

[Ubiquinone-dot]

In RF3 you can template the ligand with your input, in RFD3 you can't but it should matter less there if you're using fixed ligands - is it RF3 you're trying to use?

[AlvinAi-cloud]

Thank you for the clarification. I am using RFD3, so I guess I can ignore the warning. So in RFD3, the ligand will not use conformers, right? There will be some advantageous if the ligand can be flexible.

Btw, I found another potential bug: when H-bond acceptors/donors are specified in the input json, the output structure will be duplicated (one set in the designated folder, and another set in the fold where RFD3 is run). For the 2nd set, it is in the PDB format, and their names are not finally formatted. This doesn't cause errors, except for using more disk space.

In RF3 you can template the ligand with your input, in RFD3 you can't but it should matter less there if you're using fixed ligands - is it RF3 you're trying to use?