For many molecular designers working on DNA nanostructures, a common workflow challenge lies in translating intricate 3D models into formats that are simulation-ready. This becomes especially critical when preparing systems for coarse-grained simulations like those run with oxDNA.
Adenita, a toolkit within the SAMSON platform, offers a robust solution for modeling DNA nanostructures and exporting them into simulation-compatible formats. In this post, we walk through how export options in Adenita work, what formats are supported, and what you need to do to make your designs simulation-ready.
Export Options in Adenita
Once you’ve built your DNA nanostructure—whether from a Cadnano import, a custom strand or nanotube, or a wireframe model using the Daedalus algorithm—Adenita gives you several export paths through its main interface:
- CSV Sequence File: Outputs the sequence data for scaffolds and strands, useful for synthesis or sequence analysis workflows.
- oxDNA Format: Generates files compatible with the oxDNA simulation framework, which supports coarse-grained simulations of DNA systems.
These options are accessible via the export button:
When to Use Each Format
CSV is ideal when you’re validating base sequences or transferring designs to bioinformatics pipelines. By contrast, oxDNA is the go-to export type when setting up mechanical, thermal, or interaction-based simulations in coarse-grained environments. oxDNA is particularly valued for its speed and ability to model structural dynamics in large-scale nucleic acid systems.
What You Should Know Before Exporting
Before exporting, it’s helpful to check a few key properties of your model:
- Have you set sequences for the scaffold and complementary strands? You can assign sequences via the Set scaffold button:
- Did you define strand ends properly? Setting accurate 5’ ends is important, especially for circular structures or when merging multiple strands.
Being careful at this stage ensures oxDNA receives well-formed input, improving downstream simulation stability.
Why This Matters for Molecular Modelers
Molecular modeling often involves many passes between design and simulation. A tool like Adenita allows faster iterations because it bridges visual design and simulation preparation inside the same environment. You can go from assembling strands, to setting annotations, to preparing oxDNA-compatible output in one place. This helps streamline workflows and reduces the risk of mismatches between design intention and simulation input.
Here’s a visual overview of Adenita’s main interface, where design and export tools become accessible:
Additional Resources
If you’re new to DNA nanostructure design or to oxDNA, Adenita includes helpful video tutorials that walk through the entire process, including export. You can also consult ntthal (external tool) if you want to calculate melting temperatures and Gibbs free energies, which can be configured through Adenita’s options.
Learn more in the Adenita documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.