kperm 0.2.0

Toolkit for Analysis of Permeation Cycles in Potassium Channels

KPerm - Toolkit for Analysis of Permeation Cycles in Potassium Channels

KPerm, released together with our JCTC paper, is a Python package specifically for identifying selecivity filter occupancy in molecular dynamics (MD) simulations of potassium channels.

Installation

You are recommended to install the latest release of KPerm via pip in a virtual environment with Python >=3.8.

pip install kperm

Examples

Jupyter Notebook

• Permeation Cycle in MthK with charge-scaling

Command-line Interface

# same as Channel.run(), computing SF occuapncy and identifying permeation events
kperm run -s coord_file -f traj_1 traj_2 traj_3 ...

# speed things up if you are not interested in SF oxygen flip and water occupancy
kperm run -s coord_file -f traj_1 traj_2 traj_3 ... --noFlip --noW

# compute summary of permeation events of all selected simulations 
# use it after running "kperm run"
kperm stats -s coord_file -f traj_1 traj_2 traj_3 ...

Documentation

https://degrootlab.github.io/KPerm/

Citation

• Lam, C. K., & de Groot, B. L. (2023). Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. Journal of Chemical Theory and Computation.doi:10.1021/acs.jctc.3c00061