One common challenge molecular modelers face is sharing or analyzing detailed atom trajectories from ligand unbinding simulations. Whether you’re preparing figures for a publication, comparing alternative pathways, or running further analysis in a third-party tool, having access to the atomic trajectories along predicted ligand paths is extremely valuable. In this post, we’ll cover how to export ligand trajectories from unbinding pathways using the Ligand Path Finder and the Export Along Paths app in SAMSON.
Why trajectory export matters
Once you’ve used Ligand Path Finder to compute plausible unbinding pathways, you’re left with a set of paths where a ligand escapes from the binding site. Each path contains conformations along the route, each with its associated energy. Being able to export this for downstream work — whether structural visualization, trajectory alignment, or energetic comparisons — can save a lot of time.
But how do you actually do it?
Exporting Paths: The Basics
After running your simulations in Ligand Path Finder, go to the Results tab. You’ll see a table where each row corresponds to a predicted path. First, select the paths you’re interested in (use Ctrl/Cmd + click for multi-selection).
You now have several export options:
- Export table content: Right-click and choose Copy table content to export a snapshot of the results.
- Export energy along paths: Right-click and choose Copy path energy to get energy values for each conformation.
- Export to document: Click the Export paths button to insert the sampled trajectories directly into your SAMSON document as paths.
Exporting Atom Trajectories
What if you’re only interested in the motion of specific atoms? This is where the Export Along Paths app comes in handy.
First, install the app from the Export Along Paths extension page. Once installed:
- In the Document View, select the atoms you want to track along the path (only the relevant atoms, e.g., ligand atoms).
- Launch the Export Along Paths app.
- Choose which path(s) you want to use, the export format, and the frame interval.
- Click Export.
The app generates a file containing the trajectory of selected atoms along each chosen path. This output can be saved in formats like XYZ, CSV, or other supported trajectory formats for further analysis or visualization.
Why not export the whole simulation?
Sometimes, it’s more practical to work with reduced data: for example, just the ligand or atoms near the binding site, instead of the entire protein-ligand complex. This speeds up visualization and ensures focus on what actually matters.
Bonus: Animate Your Paths
For quick visual feedback inside SAMSON, you can also double-click on a path to play it as an animation. Additionally, accessing the path’s Inspector lets you control animation speed, color, and playback direction.
For even smoother trajectory visualization, check out the Pathlines tutorial where you can generate curved lines showing the ligand’s center of mass throughout the path.
To learn more about Ligand Path Finder, check out the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.