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README.md

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst from the Open Force Field Group

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Manuscript description

This repository describes setting up and running host-guest binding free energy calculations on cyclodextrins using the SMIRNOFF99Frosst force field.

Code and data availability

For information related to the setup and analysis of the calculations, please see:

  • GitHub repository used to convert AMBER input files from GAFF force field to SMIRNOFF99Frosst.
  • GitHub repository for setting up the attach-pull-release calculations using paprika version 0.0.3.
  • GitHub repository for analyzing the simulations and generating the plots in this manuscript.
  • GitHub repository for the Open Force Field group containing the toolkit and force field XML file.

License

License: CC BY 4.0 License: CC0 1.0

Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License (LICENSE.md), which allows reuse with attribution. Please attribute by linking to https://github.com/slochower/smirnoff-host-guest-manuscript.

Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (LICENSE-CC0.md). All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:

  • *.sh
  • *.py
  • *.yml / *.yaml
  • *.json
  • *.bib
  • *.tsv
  • .gitignore

All other files are only available under CC BY 4.0, including:

  • *.md
  • *.html
  • *.pdf
  • *.docx

Except for the following files with different licenses:

Please open an issue for any question related to licensing.

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