APBS

APBS stands for Adaptive Poisson-Boltzmann Solver.

APBS came as part of the MGLTools packages binary and commands. For instance, APBS can be used to compute the electrostatic fields of a protein.

APBS has been included in ePMV since v0.3.1b.

The plugin acts on the current molecule. Two actions can be performed:

• • you can compute the electrostatic fields of a protein by click on the run button.

If the readgrid button is checked, once the computation is done, the plugin will load the grid potential file (molname.potential.dx) and compute the isosurface for you automatically

If the readpqr button is check, the file produced by pdb2pqr will be loaded as well (molname.pqr).

The working directory of APBS is pathoMGL/apbs-molname

• • you can color a geometry using the current grid potential (have to be load in the data player of ePMV).

Specifiy the name of the geometry you want to color. For instance "MSMS-MOL1crn".

Two options are provided for the color projections: the offset to apply to the geometry normal and the coefficient to apply on the standard deviation of the grid values.

Any type of geometry (polygon/mesh) can be assign.

Examples :

Note: We to do some more test for the accuracy of the projection especially in Cinema4D where accessing vertex normals is not simple.