I tried to generate a grid for docking with Glide using the SiteMap output. I got the following warning. What does it mean? WARNING: rdmmct(): Invalid atomic number -2, at atom of mmct 8. Atomtyping, docking will be skipped, other tasks may fail.
The warning about an invalid atomic number in the receptor structure could occur if you picked a site point as the ligand while in "Molecule" picking mode, rather than "Entry" picking mode (on the Receptor tab). If you identify a site point as the ligand, then only that individual site point will be extracted from the structure, leaving dummy atoms in the active site which Glide can't handle. Using "Entry" picking mode will cause all site points in that SiteMap output entry to be selected as the 'ligand' and later extracted from the structure.