Overview

BornProfiler is a collection of scripts to set up Poisson-Boltzmann electrostatic calculations for the APBS package, in particular calculations of the electrostatic solvation free energy of an ion along a pathway in a membrane protein (the so-called Born profile).

Features

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 epsilon=2.

• Provide a path (list of coordinates) and a PQR file of the protein as input.
• 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.

[Rashin1985]

A.Rashin & B.Honig, J Phys Chem B 89 (1985), 5588

[Pliego2000]

J.R. Pliego and J.M. Riveros. Chemical Physics Letters, 332(5-6): 597–602, 2000. doi:10.1016/S0009-2614(00)01305-1.

History and Contributions

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.