Hi all. Please forgive my delay in responding. I only recently realized that this forum doesn’t automatically email me when new people post.
BlendMol 1.0 is not compatible with Blender 2.8, but BlendMol 1.1 is. I only recently published BlendMol 1.1, so I suspect you’re using the older version. You can download BlendMol 1.1 here: http://git.durrantlab.com/jdurrant/blendmol
Let me know if you run into any bugs. Much thanks for your interest!