Get charge#

import molsysmt as msm

molecular_system = msm.convert(msm.systems['T4 lysozyme L99A']['181l.h5msm'],
                               selection='molecule_type=="protein"')

charge_groups = msm.physchem.get_charge(molecular_system, element='group', definition='physical_pH7')

charge_groups
Magnitude
[0.0 0.0 0.0 0.0 -1.0 0.0 0.0 1.0 0.0 -1.0 -1.0 0.0 0.0 1.0 0.0 1.0 0.0 0.0 1.0 -1.0 0.0 -1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 -1.0 0.0 -1.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 -1.0 -1.0 0.0 -1.0 1.0 0.0 0.0 0.0 0.0 -1.0 0.0 -1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 1.0 0.0 0.0 0.0 -1.0 0.0 0.0 -1.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 1.0 0.0 -1.0 -1.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 1.0]
Unitselementary_charge
view = msm.view(molecular_system)
msm.thirds.nglview.set_color_by_value(view, values=charge_groups)

view

from openmm import app
molsys = msm.systems['Trp-Cage']['1l2y.h5msm']
openmm_topology = msm.convert(molsys, to_form='openmm.Topology')

forcefield = app.ForceField("amber14-all.xml", "amber14/tip3p.xml")
system = forcefield.createSystem(openmm_topology, nonbondedMethod=app.NoCutoff, constraints=app.HBonds)

charge_atom = msm.physchem.get_charge(openmm_topology, element='atom', definition='OpenMM')

view = msm.view(molsys, structure_indices=0)
view.clear()
msm.thirds.nglview.set_color_by_value(view, element='atom', values=charge_atom, mid_value=0.0,
                                      representation='licorice')

view

charge_system = msm.physchem.get_charge(system, element='system', definition='OpenMM')

charge_system
1.0 elementary_charge