diff --git a/modules/mol/mm/pymod/export_settings.cc b/modules/mol/mm/pymod/export_settings.cc
index 9d65cacd869e955fa5bb9235853ae69cc5907ce3..a5dfc2811936245ed4347f479af9b456c39c7749 100644
--- a/modules/mol/mm/pymod/export_settings.cc
+++ b/modules/mol/mm/pymod/export_settings.cc
@@ -52,7 +52,6 @@ void export_MMSettings()
.def_readwrite("add_nonbonded",&ost::mol::mm::MMSettings::add_nonbonded)
.def_readwrite("add_gbsa",&ost::mol::mm::MMSettings::add_gbsa)
.def_readwrite("constrain_hbonds",&ost::mol::mm::MMSettings::constrain_hbonds)
- .def_readwrite("constrain_hangles",&ost::mol::mm::MMSettings::constrain_hangles)
.def_readwrite("constrain_bonds",&ost::mol::mm::MMSettings::constrain_bonds)
.def_readwrite("rigid_water",&ost::mol::mm::MMSettings::rigid_water)
.def_readwrite("strict_interactions",&ost::mol::mm::MMSettings::strict_interactions)
diff --git a/modules/mol/mm/src/mm_settings.hh b/modules/mol/mm/src/mm_settings.hh
index 45fac0b7205cdf17f0895dff1e611f60deb90709..a4db474c9cba97def669dab03a90257d317b9ef5 100644
--- a/modules/mol/mm/src/mm_settings.hh
+++ b/modules/mol/mm/src/mm_settings.hh
@@ -64,7 +64,6 @@ struct MMSettings{
add_nonbonded(true),
add_gbsa(false),
constrain_hbonds(false),
- constrain_hangles(false),
constrain_bonds(false),
rigid_water(false),
strict_interactions(true),
@@ -109,7 +108,6 @@ struct MMSettings{
bool add_nonbonded;
bool add_gbsa;
bool constrain_hbonds;
- bool constrain_hangles;
bool constrain_bonds;
bool rigid_water;
bool strict_interactions;
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index 0c8742d9cf3022c088a3ee99910c7c36ceb9e4f3..a278b05812291955e18a0700aee60cb60b3855d0 100644
--- a/modules/mol/mm/src/topology_creator.cc
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -55,9 +55,6 @@ namespace ost{ namespace mol{ namespace mm{
TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
const MMSettingsPtr settings){
- if(settings->constrain_hangles == true && settings->constrain_hbonds == false){
- throw ost::Error("If hangles is true, hbonds must also be true in settings object!");
- }
ost::mol::ResidueHandleList res_list = ent.GetResidueList();
ost::mol::XCSEditor ed = ent.EditXCS(ost::mol::BUFFERED_EDIT);
@@ -481,7 +478,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
}
}
if(settings->rigid_water){
- if(residue_names_of_atoms[(*i)[0]] == "SOL" || residue_names_of_atoms[(*i)[1]] == "SOL"){
+ if(residue_names_of_atoms[(*i)[0]] == "SOL" && residue_names_of_atoms[(*i)[1]] == "SOL"){
if(distance_constraints.find(*i) != distance_constraints.end()) continue;
distance_constraints.insert(*i);
Real distance;
@@ -499,10 +496,10 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
if(settings->rigid_water){
for(std::set<Index<3> >::iterator i = angles.begin();
i != angles.end(); ++i){
- if(residue_names_of_atoms[(*i)[0]] == "SOL" || residue_names_of_atoms[(*i)[0]] == "SOL" ||
+ if(residue_names_of_atoms[(*i)[0]] == "SOL" && residue_names_of_atoms[(*i)[0]] == "SOL" &&
residue_names_of_atoms[(*i)[2]] == "SOL"){
- //even for ideal_bond_length_constraints, we calculate the ideal angle every time...
- //could be replaced...
+ //we only have to add the H-H distance constant, the O-H distance is already
+ //constrained above
Real distance;
if(settings->ideal_bond_length_constraints) distance = 0.15139; //HH distance taken from CHARMM
else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[2]].GetPos())/10;
@@ -511,62 +508,6 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
}
}
}
-
- if(settings->constrain_hangles){
- for(std::set<Index<3> >::iterator i = angles.begin();
- i != angles.end(); ++i){
- if(atom_masses[(*i)[0]] < 1.1 && atom_masses[(*i)[2]] < 1.1){
- //two hydrogens...
- if(constrained_angles.find(*i) != constrained_angles.end()) continue;
- Real distance;
- if(settings->ideal_bond_length_constraints){
- MMInteractionPtr bond_one = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
- MMInteractionPtr bond_two = ff->GetBond(atom_types[(*i)[1]],atom_types[(*i)[2]]);
- MMInteractionPtr angle = ff->GetAngle(atom_types[(*i)[0]],atom_types[(*i)[1]],atom_types[(*i)[2]]);
- std::vector<Real> parameters;
- Real l1,l2,a;
- parameters = bond_one->GetParam();
- l1 = parameters[0];
- parameters = bond_two->GetParam();
- l2 = parameters[0];
- parameters = angle->GetParam();
- a = parameters[0];
- distance = sqrt(l1*l1+l2*l2-2*l1*l2*cos(a));
- }
- else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[2]].GetPos())/10;
- top->AddDistanceConstraint((*i)[0],(*i)[2],distance);
- constrained_angles.insert(*i);
- continue;
- }
-
- if(atom_masses[(*i)[1]] > 15.0 && atom_masses[(*i)[1]] < 17.0){
- //central atom is an oxygen
- if(atom_masses[(*i)[0]] < 1.1 || atom_masses[(*i)[2]] < 1.1){
- //a hydrogen is attached to the oxygen...
- if(constrained_angles.find(*i) != constrained_angles.end()) continue;
- Real distance;
- if(settings->ideal_bond_length_constraints){
- MMInteractionPtr bond_one = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
- MMInteractionPtr bond_two = ff->GetBond(atom_types[(*i)[1]],atom_types[(*i)[2]]);
- MMInteractionPtr angle = ff->GetAngle(atom_types[(*i)[0]],atom_types[(*i)[1]],atom_types[(*i)[2]]);
- std::vector<Real> parameters;
- Real l1,l2,a;
- parameters = bond_one->GetParam();
- l1 = parameters[0];
- parameters = bond_two->GetParam();
- l2 = parameters[0];
- parameters = angle->GetParam();
- a = parameters[0];
- distance = sqrt(l1*l1+l2*l2-2*l1*l2*cos(a));
- }
- else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[2]].GetPos())/10;
- top->AddDistanceConstraint((*i)[0],(*i)[2],distance);
- constrained_angles.insert(*i);
- continue;
- }
- }
- }
- }
//remove all constraints from the bonds and angles
for(std::set<Index<2> >::iterator i = distance_constraints.begin();