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# Open-3SPN2
A Implementation of the 3SPN.2 and 3SPN.2C coarse-grained molecular model of DNA in OpenMM.
3SPN.2 and 3SPN.2C are DNA coarse-grained forcefields developed by the [de Pablo group](https://pme.uchicago.edu/group/de-pablo-group). Each DNA nucleotide is modelled by 3 beads: one bead for the phosphate, a second one for the sugar and a third one nucleobase. These forcefields were adapted by the [Wolynes group](https://wolynes.rice.edu/) to model protein-DNA interactions as a complement for the [AWSEM](https://github.com/npschafer/openawsem) coarse-grained protein forcefield.
## Installation
Installation of the open3SPN2 repository is available through anaconda. Some of the dependencies are contained in the omnia channel (openmm, pdbfixer) or in the conda-forge channel (mdtraj).
```conda config --append channels conda-forge```
```conda install -c wolynes-lab open3spn2```
For protein-DNA simulations you will also need to install [openAWSEM](https://github.com/npschafer/openawsem) and add the openAWSEM path to the `$PYTHONPATH` environment variable. In linux you can set the path variables on `~/.bashrc`.
```export PYTHONPATH=/path/to/openAWSEM:$PYTHONPATH```
## Documentation
Further documentation and tutorials are hosted in [readthedocs](https://open3spn2.readthedocs.io/en/latest/).
## Citations
If you publish any work using the open3SPN2 package, please include the following references:
Open3SPN2
Lu, W., Bueno, C., Schafer, N. P., Moller, J., Jin, S., Chen, X., ... & Wolynes, P. G. (2021). OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLoS computational biology, 17(2), e1008308. https://doi.org/10.1371/journal.pcbi.1008308
3SPN.2
Hinckley, D. M., Freeman, G. S., Whitmer, J. K., & De Pablo, J. J. (2013). An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization. Journal of Chemical Physics, 139(14). https://doi.org/10.1063/1.4822042
3SPN.2C
Freeman, G. S., Hinckley, D. M., Lequieu, J. P., Whitmer, J. K., & De Pablo, J. J. (2014). Coarse-grained modeling of DNA curvature. Journal of Chemical Physics, 141(16). https://doi.org/10.1063/1.4897649
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