I'm trying to place my protein and ligand complex into a protein bilayer for MD simulations. I've already used OPM to place my protein-ligand complex into a lipid bilayer.
When I upload the output pdb file from OPM into the "protein/membrane system" option, the first page that pops up is a "Model/Chain Selection Option" and tells me to "Click on the chains you want to select."
I have a tetramer system so all 4 chains were already selected, but I also have a ligand and some heteroatoms that show up.
Do I also select those too? I'm not sure what selecting these boxes does or doesn't do.

Any information on what this option is for is much appreciated.