In this section, we will learn how to compute electrostatic potentials or open potentials computed by other programs.
In this image, the ribbon is enabled, and all residues were selected and their secondary structure was assigned as "coil" from the Edit menu in order to get a worm.
The settings for electrostatic potentials can be altered in the "Electrostatic Potential" Preferences. Currently, the protein is taken to be at pH 7.0, with default protonation state for all residues. As default, only charged residues (Arg, Lsy, Glu, Asp) are taken into account, and the charges are located at the corresponding (non-H) atom positions. You may also use the partial charges of the GROMOS 43A1 force field. This is much slower, as more charged atoms are present.
Normally potentials are computed using simple coulomb interaction. This is the fastest method, but also the less accurate, as only a uniform dielectric constant is applied both for protein interior and for the solvent space. If we want to account for the different dielectric properties of the protein interior and the solvent, we have to solve the the Poisson-Boltzmann equation numerically. (This procedure in not yet implemented in SPDV, but you may display a PB-potential computed with DELPHI).
SPDBV also allows you to visualize surfaces or potentials computed with other programs: