[IMP-dev] CHARMM topology question

[Dina Schneidman <>]

Hi,

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?

I use the following code:

IMP::atom::CHARMMParameters* ff =  new
IMP::atom::CHARMMParameters(topology_file_name, parameter_file_name);
IMP::atom::CHARMMTopology* topology = ff->create_topology(mhd_);
topology->setup_hierarchy(mhd_);
IMP::ParticlesTemp bonds =  topology->add_bonds(mhd_);
IMP::ParticlesTemp angles = ff->create_angles(bonds);
IMP::ParticlesTemp dihedrals = ff->create_dihedrals(bonds);

Thanks!
Dina