I am writing to seek guidance on handling PDBs that include undefined AAs, outside of the definition below. Specifically, I encountered an issue while submitting a PDB with a coenzyme. The output displayed the message, "encountered unknown AA: XXX in the complex. Replacing it with a dash -." In an attempt to resolve this, I replaced 'XXX' with 'XAA.' Although this change ceased the warning, but it resulted in an outcome where the input ligand clashed with the coenzyme.
I would appreciate any advice or recommended practices for addressing this. Is there a preferred method to handle such PDBs in DiffDock, particularly when dealing with coenzymes or similar cases?
I am writing to seek guidance on handling PDBs that include undefined AAs, outside of the definition below. Specifically, I encountered an issue while submitting a PDB with a coenzyme. The output displayed the message, "encountered unknown AA: XXX in the complex. Replacing it with a dash -." In an attempt to resolve this, I replaced 'XXX' with 'XAA.' Although this change ceased the warning, but it resulted in an outcome where the input ligand clashed with the coenzyme.
I would appreciate any advice or recommended practices for addressing this. Is there a preferred method to handle such PDBs in DiffDock, particularly when dealing with coenzymes or similar cases?
Thank you for your assistance.
https://github.com/gcorso/DiffDock/blob/bc6b5151457ea5304ee69779d92de0fded599a2c/utils/inference_utils.py#L14-L40