I want to add bonds, angles and dihedrals to my structure. It has some
missing atoms, but I don't want them there on purpose.
When I create the topology, those atoms are automatically added to the
structure.
Is there a way to tell it not to add any missing atoms?
When in doubt, read the documentation. ;)
topology->setup_hierarchy(mhd_);
This is for the common use case "tidy up the hierarchy so it matches the
topology, by adding/removing atoms as necessary". If you don't want to
do that, call the functions it calls yourself, leaving out
add_missing_atoms().