Electrostatic Potential Surface Panel
Calculate the electrostatic potential on a grid, using a Poisson-Boltzmann solver with the partial charges of the input structure, and generate isosurfaces and a mapping to the molecular surface.
To open this panel, click the Tasks button and browse to Structure Analysis → Poisson-Boltzmann ESP.
- Using
- Features
- Additional Resources
Using the Electrostatic Potential Surface Panel
The electrostatic potential is generated by solving the Poisson-Boltzmann equations, using the partial charges of all the atoms in the entry that is in the Workspace, which must be a single, named entry. Two grids are used—a fine grid for the region of interest ("focusing" grid) that is defined by an atom selection, and a coarse grid for the rest of the system. The structure in the Workspace is considered to be immersed in a solvent, whose parameters you can specify; the default is water.
Once the potential is evaluated, surfaces are generated by interpolation on the grid. If a mapping to the molecular (Connolly) surface is needed, this surface is also generated.
For a more accurate, quantum-mechanical ESP surface, you can run a Jaguar calculation to generate the ESP.
Electrostatic Potential Surface Panel Features
- Atoms for electrostatic potential grid section
- Solute dielectric constant text box
- Solvent dielectric constant text box
- Solvent radius text box
- Temperature text box
- Grid extension text box
- Output section
- Create Surface button
- Atoms for electrostatic potential grid options
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Choose an option for the atoms that define the fine (focusing) grid used in the Poisson-Boltzmann calculation, from All or Selected atoms. You can select the atoms in the Workspace with the usual selection tools.
- Solute dielectric constant text box
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Specify the dielectric constant for the solute (the structure for which the potential is being calculated) in this text box. You should not normally have to change it from the default value of 1.0.
- Solvent dielectric constant text box
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Specify the dielectric constant for the solvent. The default value is 80.0, corresponding to water as the solvent. For the electrostatic potential in a vacuum, set the value to 1.
- Solvent radius text box
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Specify the radius of the solvent molecules. The default value of 1.4 is the value for water.
- Temperature text box
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Set the temperature at which the calculation is performed.
- Grid extension text box
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Set the distance from the selected atoms to the edge of the grid for the electrostatic potential, in angstroms. This is the minimum distance from any atom to the edge of the grid box. Increasing this value allows isosurfaces of the potential to cover a greater extent.
- Output section
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In this section you can specify the form of the output. The electrostatic potential is calculated on a grid (producing a volume), which can be displayed in more than one way.
- ESP mapped on molecular surface option
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Map the values of the electrostatic potential onto the molecular surface for the Workspace atoms, which is also calculated.
- Surface resolution option menu
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The surface is created using interpolation on a cubic grid. This option menu allows you to specify the resolution of the resulting surface. Higher resolution means a smoother surface, which is slower to generate and draw. Lower resolution means a rougher surface but faster to generate and draw (and hence rotating will be faster). When you choose Low, Medium, or High, the grid spacing in angstroms is displayed in the text box to the right. The default choice is Automatic, which selects high resolution for less than 1000 atoms, medium for less than 10000 atoms, and low for more atoms. If you want to specify the grid spacing, choose Custom and enter the desired value in the text box.
- Electrostatic potential isosurfaces option
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Generate isosurfaces of the electrostatic potential, one for positive values and one for negative values.
- Initial isosurface value option menu
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Choose the initial isovalue for the surfaces, in units of kT/e, from this option menu. Surfaces are generated for these isovalues, but you can change them in the Manage Surfaces panel.
- Create Surface button
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Create the surface. There might be a small delay while the surface is created if you have a lot of atoms in the entry used for the surface.