I just set up LigandMPNN for the first time, and I ran into the following issue: the newest version of setuptools (v82.0.0) doesn't have pkg_resources anymore, which LigandMPNN needs. Therefore, when you create the conda environment, you have to specify the version of setuptools to use:
conda create -n ligandmpnn_env python=3.11 setuptools=81.0.0
It might be a good idea to update the readme, especially for us newbies!