openforcefield.utils.structure.merge_system(topology0, topology1, system0, system1, positions0, positions1, label0='AMBER system', label1='SMIRNOFF system', verbose=True)[source]

Merge two given OpenMM systems. Returns the merged OpenMM System.

topology0 : OpenMM Topology

Topology of first system (i.e. a protein)

topology1 : OpenMM Topology

Topology of second system (i.e. a ligand)

system0 : OpenMM System

First system for merging (usually from AMBER)

system1 : OpenMM System

Second system for merging (usually from SMIRNOFF)

positions0 : simtk.unit.Quantity wrapped

Positions to use for energy evaluation comparison

positions1 (optional) : simtk.unit.Quantity wrapped (optional)

Positions to use for second OpenMM system

label0 (optional) : str

String labeling system0 for output. Default, “AMBER system”

label1 (optional) : str

String labeling system1 for output. Default, “SMIRNOFF system”

verbose (optional) : bool

Print out info on topologies, True/False (default True)

topology : OpenMM Topology
system : OpenMM System
positions: unit.Quantity position array