Restraining receptor in trailblaze is off by default
@@ -2471,7 +2471,7 @@ class ExperimentBuilder(object):
distributed_args=experiments_to_generate,
send_results_to=None, group_size=1, sync_nodes=True)
- def _generate_experiment_protocol(self, experiment, constrain_receptor=True,
+ def _generate_experiment_protocol(self, experiment, constrain_receptor=False,
n_equilibration_iterations=None, **kwargs):
"""Generate auto alchemical paths for the given experiment.
@@ -2483,7 +2483,7 @@ class ExperimentBuilder(object):
A tuple with the experiment path and the experiment description.
constrain_receptor : bool, optional
If True, the receptor in a receptor-ligand system will have its
- CA atoms constrained during optimization (default is True).
+ CA atoms constrained during optimization (default is False).
n_equilibration_iterations : None or int
The number of equilibration iterations to perform before running
the path search. If None, the function will determine the number
@@ -2598,14 +2598,14 @@ class ExperimentBuilder(object):
# Restrain the receptor heavy atoms to avoid drastic
# conformational changes (possibly after equilibration).
- if len(phase.topography.receptor_atoms) != 0 and constrain_receptor:
- receptor_atoms_set = set(phase.topography.receptor_atoms)
+ if len(phase_factory.topography.receptor_atoms) != 0 and constrain_receptor:
+ receptor_atoms_set = set(phase_factory.topography.receptor_atoms)
# Check first if there are alpha carbons. If not, restrain all carbons.
- restrained_atoms = [atom.index for atom in phase.topography.topology.atoms
+ restrained_atoms = [atom.index for atom in phase_factory.topography.topology.atoms
if atom.name is 'CA' and atom.index in receptor_atoms_set]
if len(restrained_atoms) == 0:
# Select all carbon atoms of the receptor.
- restrained_atoms = [atom.index for atom in phase.topography.topology.atoms
+ restrained_atoms = [atom.index for atom in phase_factory.topography.topology.atoms
if atom.element.symbol is 'C' and atom.index in receptor_atoms_set]
mmtools.forcefactories.restrain_atoms(thermodynamic_state, sampler_state,
restrained_atoms, sigma=3.0*unit.angstroms)
