Calculate pragmatic relaxation rates of fluorinated biomolecules from molecular dynamics trajectories.

This repository is associated with the following publication:

• DT Yang, AM Gronenborn, LT Chong, “Integrating Fluorinated, Aromatic Amino Acids into the Framework of the AMBER ff15ipq Force Field.” J. Phys. Chem. A 2022, in press; https://doi.org/10.1021/acs.jpca.2c00255

This package reqiures the following:

• Numpy
• MDAnalysis
• Matplotlib
• Pandas
• Scipy

Features should be developed on branches. To create and switch to a branch, use the command:

git checkout -b new_branch_name

To switch to an existing branch, use:

git checkout branch_name

To submit your feature to be incorporated into master branch, you should submit a Pull Request. The repository maintainers will review your pull request before accepting your changes.

Usage Examples

To run for 4F-Trp using the provided example simulation data:

python fluorelax.py -c data/3k0n_w4f_frame_198ns_dry.nc -p data/3k0n_w4f_dry.prmtop --sys w4f

To view all available arguments and descriptions:

python fluorelax.py --help

Copyright

Copyright (c) 2021, Darian Yang