diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc index a278b05812291955e18a0700aee60cb60b3855d0..2f46a885e095831fbdcdeec84e37cc3748f8a2ff 100644 --- a/modules/mol/mm/src/topology_creator.cc +++ b/modules/mol/mm/src/topology_creator.cc @@ -224,7 +224,6 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent, std::vector<Real> atom_charges; std::vector<String> atom_names; std::vector<Real> atom_masses; - std::vector<String> atom_elements; std::vector<String> residue_names_of_atoms; ost::mol::AtomHandleList bonded_atoms; std::vector<uint> temp; @@ -236,7 +235,6 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent, i!=atom_list.end();++i){ residue_index = residue_indices[i->GetResidue().GetHashCode()]; residue_names_of_atoms.push_back(i->GetResidue().GetName()); - atom_elements.push_back(i->GetElement()); atom_types.push_back(building_blocks[residue_index]->GetType(i->GetName())); atom_charges.push_back(building_blocks[residue_index]->GetCharge(i->GetName())); atom_masses.push_back(ff->GetMass(atom_types.back())); @@ -462,8 +460,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent, continue; } if(settings->constrain_hbonds){ - //if(atom_elements[(*i)[0]] == "H" || atom_elements[(*i)[1]] == "H"){ - if(atom_masses[(*i)[0]] < 1.1 || atom_masses[(*i)[1]] < 1.1){ + if(atom_names[(*i)[0]][0] == 'H' || atom_names[(*i)[1]][0] == 'H'){ if(distance_constraints.find(*i) != distance_constraints.end()) continue; distance_constraints.insert(*i); Real distance;