Get mass#
import molsysmt as msm
molsys = msm.convert(msm.systems['T4 lysozyme L99A']['181l.h5msm'])
msm.info(molsys)
| form | n_atoms | n_groups | n_components | n_chains | n_molecules | n_entities | n_waters | n_ions | n_small_molecules | n_proteins | n_structures |
|---|---|---|---|---|---|---|---|---|---|---|---|
| molsysmt.MolSys | 1441 | 302 | 141 | 6 | 141 | 5 | 136 | 2 | 2 | 1 | 1 |
mass_atoms = msm.physchem.get_mass(molsys, element='atom', selection='molecule_type=="protein"')
mass_atoms
| Magnitude | [14.007 12.011 12.011 ... 12.011 12.011 14.007] |
|---|---|
| Units | unified_atomic_mass_unit |
mass_groups = msm.physchem.get_mass(molsys, element='group', selection='molecule_type=="protein"')
mass_groups
| Magnitude | [122.12099999999998 108.056 102.072 138.105 122.059 122.12099999999998 102.072 144.093 102.072 110.048 122.059 54.028 102.072 144.093 102.072 116.07900000000001 102.072 154.10399999999998 116.07900000000001 110.048 94.04899999999999 122.059 54.028 154.10399999999998 154.10399999999998 94.04899999999999 102.072 54.028 102.072 54.028 130.08599999999998 102.072 102.072 94.04899999999999 116.07900000000001 82.038 90.06099999999999 82.038 102.072 108.056 66.039 66.039 116.07900000000001 82.038 122.059 102.072 110.048 116.07900000000001 66.039 102.072 54.028 144.093 108.056 94.04899999999999 108.056 54.028 90.06099999999999 102.072 94.04899999999999 116.07900000000001 110.048 122.059 66.039 122.059 116.07900000000001 102.072 138.105 108.056 120.06700000000001 110.048 90.06099999999999 110.048 66.039 66.039 90.06099999999999 144.093 54.028 102.072 102.072 144.093 108.056 66.039 116.07900000000001 102.072 116.07900000000001 90.06099999999999 90.06099999999999 154.10399999999998 110.048 82.038 102.072 110.048 66.039 90.06099999999999 144.093 144.093 66.039 66.039 66.039 102.072 108.056 122.12099999999998 90.06099999999999 138.105 120.06700000000001 122.12099999999998 54.028 122.059 94.04899999999999 54.028 90.06099999999999 66.039 54.028 138.105 94.04899999999999 108.056 82.038 102.072 144.093 122.12099999999998 102.072 120.06700000000001 120.06700000000001 116.07900000000001 144.093 176.134 110.048 122.059 66.039 66.039 90.06099999999999 108.056 102.072 66.039 116.07900000000001 82.038 144.093 176.134 154.10399999999998 108.056 120.06700000000001 94.04899999999999 90.06099999999999 108.056 144.093 66.039 116.07900000000001 144.093 90.06099999999999 102.072 94.04899999999999 94.04899999999999 138.105 144.093 94.04899999999999 54.028 94.04899999999999 176.134 110.048 66.039 154.10399999999998 116.07900000000001] |
|---|---|
| Units | unified_atomic_mass_unit |
msm.physchem.get_mass(molsys, element='system')
19463.619999999995 unified_atomic_mass_unit
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)
msm.physchem.get_mass(system, element='system', method='OpenMM')
2170.4500000000016 unified_atomic_mass_unit