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https://github.com/Psivant/femto
A comprehensive toolkit for predicting free energies
https://github.com/Psivant/femto
Last synced: 14 days ago
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A comprehensive toolkit for predicting free energies
- Host: GitHub
- URL: https://github.com/Psivant/femto
- Owner: Psivant
- License: mit
- Created: 2023-12-07T15:28:18.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2024-08-26T22:49:42.000Z (3 months ago)
- Last Synced: 2024-08-27T17:29:25.123Z (3 months ago)
- Language: Python
- Homepage: https://psivant.github.io/femto/
- Size: 2.3 MB
- Stars: 46
- Watchers: 2
- Forks: 5
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Free Energy and MD Toolkit using OpenMM
A comprehensive toolkit for predicting free energies
---
The `femto` framework aims to offer not only a compact and comprehensive toolkit for predicting binding free energies
using methods including `ATM` and `SepTop`, but also a full suite of utilities for running advanced simulations using
OpenMM, including support for HREMD and REST2.
_**Warning:** The ATM implementation was recently updated to make use of the new `ATMForce` shipped with OpenMM 8.1.
While every effort was made to ensure correctness, this was a major change that is still being tested and there may
be bugs. Please report any issues you encounter._
_Further, the default protocols selected for the ATM and SepTop methods are still being tested and optimized, and may
not be optimal. It is recommended that you run a few test calculations to ensure that the results are reasonable._
## Installation
This package can be installed using `conda` (or `mamba`, a faster version of `conda`):
```shell
mamba install -c conda-forge femto
```
If you are running with MPI on an HPC cluster, you may need to instruct conda to use your local installation
depending on your setup
```shell
mamba install -c conda-forge femto "openmpi=4.1.5=*external*"
```
where in this example you should change `4.1.5` to match the version of OpenMPI installed on your cluster / machine.
## Getting Started
To get started, see the [usage guide](https://psivant.github.io/femto/latest/guide-md).
## Acknowledgements
This framework benefited hugely from the work of Psivant's [Open Science Fellows](https://psivant.com/company/open-science-fellows/).
### ATM
The ATM implementation is based upon the work and advice of E. Gallicchio _et al_:
* [Wu, Joe Z., et al. "Alchemical transfer approach to absolute binding free energy estimation." Journal of Chemical Theory and Computation 17.6 (2021): 3309-3319.](https://pubs.acs.org/doi/10.1021/acs.jctc.1c00266)
* [Azimi, Solmaz, et al. "Relative binding free energy calculations for ligands with diverse scaffolds with the alchemical transfer method." Journal of Chemical Information and Modeling 62.2 (2022): 309-323.](https://pubs.acs.org/doi/full/10.1021/acs.jcim.1c01129)
### SepTop
The SepTop implementation is based upon the work and advice of H. M. Baumann, D. L. Mobley _et al_:
* [Rocklin, Gabriel J., David L. Mobley, and Ken A. Dill. "Separated topologies—A method for relative binding free energy calculations using orientational restraints." The Journal of chemical physics 138.8 (2013).](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598757/)
* [Baumann, Hannah M., et al. "Broadening the scope of binding free energy calculations using a Separated Topologies approach." Journal of Chemical Theory and Computation 19.15 (2023): 5058-5076.](https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00282)