diff --git a/vermouth/rcsu/go_pipeline.py b/vermouth/rcsu/go_pipeline.py index 4312bd566..1917cb178 100644 --- a/vermouth/rcsu/go_pipeline.py +++ b/vermouth/rcsu/go_pipeline.py @@ -40,8 +40,6 @@ def prepare_run(self, system, moltype): vermouth.MergeAllMolecules().run_system(system) molecule = system.molecules[0] molecule.meta['moltype'] = moltype - # add citations for the go model here - molecule.citations.add('M3_GO') def run_system(self, system, **kwargs): self.kwargs = kwargs diff --git a/vermouth/rcsu/go_vs_includes.py b/vermouth/rcsu/go_vs_includes.py index 2e2249d92..1d1d44365 100644 --- a/vermouth/rcsu/go_vs_includes.py +++ b/vermouth/rcsu/go_vs_includes.py @@ -40,7 +40,7 @@ class VirtualSiteCreator(Processor): Assign molecule type names to the molecules in a system. :func:`add_virtual_sites` """ - def __init__(self, go_anchor_bead, go_atomname): + def __init__(self, go_anchor_bead='BB', go_atomname='CA'): self.system = None self.backbone = go_anchor_bead self.atomname = go_atomname @@ -52,6 +52,8 @@ def run_molecule(self, molecule): if not self.system: raise ValueError('This processor requires a system.') + # add citations for the go model here + molecule.citations.add('M3_GO') self.add_virtual_sites(molecule, prefix=moltype, @@ -65,7 +67,7 @@ def run_system(self, system): LOGGER.info("Adding Virtual Sites to backbone beads.", type="step") super().run_system(system) - def add_virtual_sites(self, molecule, prefix, backbone='BB', atomname='CA', charge=0): + def add_virtual_sites(self, molecule, prefix, backbone, atomname, charge=0): """ Add the virtual sites for GoMartini in the molecule.