Calculating Electrostatics

Adaptive Poisson-Boltzmann Solver (APBS) is a software package for modeling biomolecular solvation by solving the Poisson-Boltzmann equation (PBE). The PBE is a popular continuum model used to describe electrostatic interactions between solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including:

  • Simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics,
  • Implicit solvent molecular dynamics of biomolecules,
  • Solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and
  • Biomolecular titration studies.

APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. We also provide implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions.

How to calculate Electrostatics:

Web

After you have set up your structures through the Getting Structures Ready page, you will see a link to run your results with the APBS web solver. Follow that link and you will be directed to the APBS web page. Press “Launch” to run APBS using the input file generated by the PDB2PQR web server, or click on the check box to see the advanced options (shown below).

Command Line

Using the APBS input file generated by PDB2PQR (either through the command line or downloaded from the web server), you can run APBS directly from the command line as follows:

% apbs 1FAS.in

PyMOL APBS plugin

The PyMOL molecular graphics software package can both run APBS and visualize resulting electrostatic potentials.
Below are instructions for performing a basic demonstration of how to go from a PDB entry to a plot of structure and potential in PyMOL using APBS.

Generating the PQR

Generate the PQR file using the steps outlined in Getting Structures Ready We’ll continue the example with fasciculin-2 (PDB ID 1FAS), a snake neurotoxin which binds the negatively-charged acetylcholinesterase.

Load the PQR file you created into PyMOL (File → Open…) and choose your favorite graphical representation of the molecular structure.

Performing the electrostatics calcuation

Go to the Plugin → APBS Tools… to open the APBS calculation plugin.

  • Under the “Main” tab of the PyMOL APBS Tools window, select Use another PQR and either browse to (via the Choose Externally Generated PQR: button) or input the path to your PQR file. This step is necessary to ensure you use the radii and charges assigned by PDB2PQR.

  • Under the “APBS Location” tab of the PyMOL APBS Tools window, either browse to (via the APBS binary location: button) or input the path to your local APBS binary. It is not necessary to provide a path to the APBS psize.py binary for most biomolecules.

  • Under the “Temporary File Locations” tab of the PyMOL APBS Tools window, customize the locations of the various temporary files created during the run. This can be useful if you want to save the generated files for later use.

  • Under the “Configuration” tab of the PyMOL APBS Tools window, hit the Set grid to set the grid spacings. The default values are usually sufficient for all but the most highly charged biomolecules.

  • Under the “Configuration” tab of the PyMOL APBS Tools window, customize the remaining parameters; the defaults are usually OK.

  • Under the “Configuration” tab of the PyMOL APBS Tools window, hit the Run APBS button to start the APBS calculation. Depending on the speed of your computer, this could take a few minutes. The Run APBS button will become unselected when the calculation is finished.

Note that 0.150 M concentrations for the +1 and −1 ion species are often useful to ensure that electrostatic properties are not overly exaggerated.