Designing DNA nanostructures is often only the beginning of a molecular modeling workflow. Whether you’re crafting wireframe geometries or constructing detailed double-stranded models, the next step is frequently simulation—one of the most powerful ways to assess stability, dynamics, or interactions. But many researchers encounter a recurring pain point: how to effectively export designed DNA structures for simulation tools like oxDNA.
This blog post covers how you can export your DNA nanostructures from Adenita—a SAMSON Extension—for simulations using the widely-used oxDNA format. We’ll walk through what options are available in Adenita, what formats you can generate, and how to ensure your export fits your simulation goals.
Why Use oxDNA?
oxDNA is a coarse-grained molecular dynamics simulation tool specifically developed to simulate nucleic acid nanostructures. It allows users to explore thermodynamics and kinetic properties of DNA assemblies with reduced computational cost.
If you’ve designed a structure in Adenita—such as a nanotube, lattice, or a custom wireframe object—the ability to quickly export it to oxDNA format saves considerable manual work and reduces chances for error during format conversion.
Exporting from Adenita
Once your DNA nanostructure is ready in Adenita, exporting to oxDNA format is available through the main interface. Simply locate the Export option (represented by this icon:
This option lets you generate:
- CSV sequences for record keeping or further analysis
- oxDNA files containing the structure and sequence information necessary for simulations
Tip: Make sure all components you want to export are part of your DNA nanostructure and have assigned sequences, especially scaffolds and staples. Otherwise, the export may be incomplete or syntactically invalid for oxDNA.
Preparation Steps Before Export
Before you initiate an export, consider doing the following:
- Check and assign sequences using the Set Scaffold button
. - Use the Calculate option
to verify melting temperatures and Gibbs free energies (optional but useful for refinement). - Ensure your design uses supported nucleotide arrangements optimized for oxDNA’s modeling conventions.
Once Exported…
The oxDNA files generated by Adenita can then be loaded into various oxDNA simulation setups. Popular options include:
- oxDNA command-line tools
- Visualization with oxView
- Custom processing pipelines using Python tools like oxdna-analysis
Conclusion
The ability to simulate DNA nanostructures is crucial for any molecular modeler exploring behavior beyond static design. Adenita’s built-in export to oxDNA format bridges the gap between 3D modeling and dynamic simulation, removing friction and making it easier to get insight from your structures.
To learn more, visit the full documentation for Adenita.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.