Running DNA nanostructure simulations can be a powerful way to test your designs before heading to the lab. But exporting complex DNA models for use in simulation tools like oxDNA can feel like a hurdle—especially when dealing with 3D nanostructures built from scratch or imported from other platforms. If you’ve ever asked yourself: “How do I get this DNA model into a format my simulation framework accepts?” — you’re not alone.
Adenita, a SAMSON Extension for DNA nanostructure design, offers a streamlined export feature that helps you go from visual, interactive design to simulation-ready data with minimal friction. Whether you’re working with wireframes, lattices, or nanotubes, you can export your models in formats supported by oxDNA or as a CSV list of sequences.
Why this matters
Exporting correctly formatted DNA structures is essential for:
- Validating designs under different thermal, chemical, or mechanical conditions through simulation tools.
- Preparing inputs for coarse-grained molecular dynamics workflows.
- Sharing sequence and structure information with collaborators for experimental workflows.
How It Works in Adenita
Once you’ve constructed your DNA nanostructure in Adenita, exporting is straightforward. Here’s a step-by-step walkthrough:
- Open your design in Adenita within SAMSON.
- Click on the
Export button in Adenita’s main interface. - Choose one of the export options:
- Sequence (.csv) – Ideal for generating a list of DNA sequences used in your model.
- oxDNA Format – Prepares files to be read by the oxDNA simulation framework.
- Save the file to your local folder, and you’re ready to start simulating or sharing.
Things to Keep in Mind
- Adenita assigns sequences automatically when scaffolds are created. You can edit or reassign these sequences in the interface before exporting.
- If you’re exporting to oxDNA, ensure all your design components have defined sequences. Missing sequences may cause simulation errors or incomplete models.
- Depending on your design complexity, oxDNA export files may be large. Consider breaking your model into components using the
.adnpartformat if needed.
Where to Go from Here
Now that you know how to get your models out of Adenita and into simulation, you can begin testing DNA folding, verifying self-assembly, or exploring structure stability—right from your desktop. Combined with other SAMSON tools, this makes for a flexible and efficient in-silico workflow for molecular designers and DNA nanotech researchers.
Want to dive deeper into Adenita’s tools and capabilities? Check out the full documentation:
https://documentation.samson-connect.net/tutorials/adenita/adenita/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.