A small Python package to set up "Born" calculations of an ion in a membrane protein and calculate the electrostatic free energy with APBS.

The BornProfiler package helps setting up Poisson-Boltzmann calculations of the electrostatic potential of mean force of an ion in a pore or channel under the influence of a membrane. The membrane is modelled as a dielectric slab of ε=2.

• Provide a path (list of coordinates) and a PQR file of the protein as input.
• 1D (linear) traditional Born profiles (e.g. ion in channel)
• 3D (spatial) solvation free energy maps [Stelzl2014]
• A membrane can be defined with arbitrary thickness, z-position, and dielectric. A headgroup region can also be defined with a different dielectric constant.
• Define all input parameters in a compact parameter file so that there is always a record of the exact calculation setup available.
• Born radii for all ions from the Rashin & Honig paper [Rashin1985] are included; just select the ion in the input file.
• Born radii for H3O+, OH- (and H+... for testing) have been derived from the solvation free energies in [Pliego2000] directly via the Born equation. USE AT YOUR OWN RISK!!
• Customize run scripts and queuing system submission scripts by providing your own templates.

References

Based on Kaihsu Tai's Python rewrite (Poisson-Boltzmann profile for an ion channel) of the original placeion.sh and analyze.sh bash scripts by Kaihsu Tai and Oliver Beckstein.

Uses material from the APBS Wiki (PMF of a helix in a membrane) and contains a modified version of Michael Grabe's draw_membrane2 from APBSmem.

See the file AUTHORS for all contributors.