.. -- coding: utf-8 --

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README for BornProfiler

|docs|

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

.. _APBS: https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html

.. 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.

.. rubric:: 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.

.. _Poisson-Boltzmann profile for an ion channel:
http://en.wikiversity.org/wiki/Poisson%E2%80%93Boltzmann_profile_for_an_ion_channel

.. _PMF of a helix in a membrane:
https://sites.google.com/a/poissonboltzmann.org/software/apbs/examples/potentials-of-mean-force/the-polar-solvation-potential-of-mean-force-for-a-helix-in-a-dielectric-slab-membrane

.. _Apbsmem:
https://apbsmem.sourceforge.io/

.. |docs| image:: https://readthedocs.org/projects/bornprofiler/badge/?version=latest
:target: https://bornprofiler.readthedocs.io/en/latest/?badge=latest
:alt: Documentation