README for BornProfiler

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

Warning

This software is under development and should not be relied upon yet. Feedback in the form of bug reports and pull requests is welcome.

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 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

[Stelzl2014]

LS Stelzl, PW Fowler, MSP Sansom, O Beckstein. J Mol Biol 426 (2014), 735-751.

[Rashin1985]

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

[Pliego2000]

J.R. Pliego and J.M. Riveros. Chemical Physics Letters 332 (2000), 597--602. 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.

See the file AUTHORS for all contributors.