CHARMM Development Project Forums User Discussion & Questions Setup, I/O, and Basic questions Selecting only lipids under protein

I agree, for many analyses of solvent behavior around a solute the existing tools (COOR ANALysis or SHELL) do a very good job. For the kinds of analyses indicated by the original poster a CHARMM loop is likely to be the better solution; in particular since the concept of "under" is not so clearly tied to "being close to".