Electrostatic potential maps
The molecular electrostatic potential (MEP) shows the electrostatic potential on the molecular surface. MEP illustrates the charge distributions of molecules three dimensionally.
Quantum chemical methods
One can obtain the eletrostatic potential by DFT calculation using softwares, e.g. CP2K or Gaussian. Here is an example of H2O. The h2o-hartree.cube file is the electrostatic potential calculated by DFT.
Example in Python
>>> from batoms import Batoms
>>> from ase.io.cube import read_cube_data
>>> bpy.ops.batoms.delete()
>>> hartree, atoms = read_cube_data('../tests/datas/h2o-hartree.cube')
>>> batoms = Batoms("h2o", from_ase=atoms)
>>> # add volumetric data
>>> batoms.volumetric_data['hartree'] = -hartree
>>> # set probe to 0 for the Van der Waals surface
>>> batoms.molecular_surface.settings['1'].probe = 0
>>> # color the molecular surface by the volumetric data
>>> batoms.molecular_surface.settings['1'].color_by = 'hartree'
>>> batoms.molecular_surface.draw()
>>> batoms.get_image([-1, 0, 0], output="h2o-MEP.png")
Example in GUI
In Molecular surface panel, one can choose ‘hartree’ for the coloring in color_by.
Classic method
Here is a fast way to calculate electrostatic potential maps using classic method, in which the electrostatic potential is calculated using the atomic partial charges. We estimates the atomic partial charges based on MMFF94 force field using openbabel.
Example in Python
Here is an example of H2O.
>>> from batoms import Batoms
>>> from ase.io.cube import read_cube_data
>>> bpy.ops.batoms.delete()
>>> bpy.ops.batoms.molecule_add(label='h2o', formula='H2O')
>>> batoms = Batoms("h2o")
>>> # set probe to 0 for the Van der Waals surface
>>> batoms.molecular_surface.settings['1'].probe = 0
>>> # color the molecular surface by the volumetric data
>>> batoms.molecular_surface.settings['1'].color_by = 'Electrostatic_Potential'
>>> batoms.molecular_surface.draw()
>>> batoms.get_image([-1, 0, 0], output="h2o_MEP_classic.png")
Example in GUI
In Molecular surface panel, one can choose ‘Electrostatic_Potential’ for the coloring in color_by.