A tutorial for Grid Inhomogenous Solvation Theory (GIST) as implemented in AmberTool's cpptraj. The tutorial aims to teach how to apply GIST for small molecules and proteins, with biotin-streptavidin as a showcase example.
The current version of the manuscript is found in manuscript/manuscript.pdf.
The manuscript is not currently published, but is aimed at the Living Journal of Computational Molecular Science.
As such, the tutorial is developed in line with LiveCoMS guidelines on Paper Writing as Code Development and will be further updated in correspondence with the community. If you notice any issues or have suggestions, please raise them as an Issue or write up a Pull Request.
- cpptraj (Version 6.24 or higher)
- gisttools (Version 0.2 or higher)
- mdtraj (Version 1.9.7 or higher)
- numpy (Tested with version 1.23.5)
- pandas (Tested with version 1.5.3)
The tutorial code is provided as a Jupyter Notebook at code/tutorial-gist.ipynb.
We recommend using JupyterLab or VS Code (with the Jupyter extensions) for editing and working with the notebook.
Molecular visualisations are generated with PyMol and input scripts are provided in the output/visualization folder.
In the same order as in the manuscript:
- Valentin J Hoerschinger
- Franz Waibl
- Vjay Molino
- Helmut Carter
- Monica L Fernández-Quintero
- Steven Ramsey
- Daniel R Roe
- Klaus R Liedl
- Michael K Gilson
- Tom Kurtzman
The repository is currently managed by Valentin (@vhoer).