Re: [IMP-dev] CHARMM topology question

On 8/15/12 11:57 AM, Dina Schneidman wrote: > 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().

Ben