Is it possible to put Protein as a Ligand ?

[parkjooyoung99]

Hi, thank you for sharing your script of doing protein docking.

I am currently working with protein-protein interaction, and am trying to use your codes on my alphafold3 predicted structure. However, whenever I try to put protein as a ligand, it generates an error of 'UndefinedStereochemistryError' like below screenshot:

I have tested it with one of the protein from PDB (1io1) but still having the same problem, assuming this is happening since ligand is set as protein not small molecules.

Is it impossible to use protein as a ligand??

Thank you.

Best, JY Park

[tdudgeon]

OpenMM can support modelling protein-protein interactions, but the scripts in this repo are specific for modelling small molecule ligands.