Published January 24, 2023
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Molecular dynamics study of Cl− permeation through cystic fibrosis transmembrane conductance regulator (CFTR)
Authors/Creators
- 1. University of Toronto; The Hospital for Sick Children
- 2. Dalhousie University
Description
This record contains some files corresponding to some workflows used in our published journal article "Molecular dynamics study of Cl− permeation through cystic fibrosis transmembrane conductance regulator (CFTR)" (DOI: 10.1007/s00018-022-04621-7)
Some files that are used to perform analysis that are not part of the standard analysis of MD are provided here. An example is the MOLE2 analysis -- because it is the only program I found that worked on path detection and parametrization in this channel.
Notes
In this repository there are:
mdp files: for equilibration and production runs. One of the production runs have electric field
gro files: CFTR protein states to aid orienting and aligning before applying analysis scripts
tcl files: mainly pertains to the analysis of ions inside the pore
MOLE2 related files: parameters are in "input.xml"; running MOLE2 using shell script "mole2tunnel.sh"; "mole2.py" has functions that help parse outputs of MOLE2
We are experimenting this format of standardized repositories for research work. For inquiries, contact author Zhi Wei Zeng at wilson.zeng@mail.utoronto.ca
Files
input.xml
Files
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Additional details
Related works
- Is cited by
- Journal article: 10.1007/s00018-022-04621-7 (DOI)