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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. 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 to model protein-DNA interactions as a complement for the AWSEM 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 omnia

conda config --append channels conda-forge

conda install -c wolynes-lab open3spn2

It is also necessary to install X3DNA >= 2.4 and set the environment variable $X3DNA to the location of the installation folder.For protein-DNA simulations you will also need to install openAWSEM and add the openAWSEM path to the $PYTHONPATH environment variable. In linux you can set the path variables on ~/.bashrc.

export X3DNA=/path/to/x3dna-v2.4

export PYTHONPATH=/path/to/openAWSEM:$PYTHONPATH

Note: open3SPN2 requires the installation of openMM. As of Feb 10 2020, openMM requires 3.5 <= python <= 3.7 and 7.5 <= CUDA <= 10.1.

Documentation

Further documentation and tutorials are hosted in readthedocs.

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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