When studying ligand migration or unbinding processes in proteins, it’s often essential to extract and analyze the precise atomic trajectories along the computed paths. Whether you’re feeding the data into further simulations, building visualizations, or compiling a presentation, being able to export these trajectories is a practical need in molecular modeling.
If you’re using the Ligand Path Finder app in SAMSON, there’s a straightforward way to export trajectories of selected atoms along computed ligand unbinding pathways. This post walks you through how to do that using the Export Along Paths app.
Why export atom trajectories?
Imagine you’ve used Ligand Path Finder to identify exit pathways for a ligand from a binding pocket. You now want to:
- Visualize the motion of specific atoms across these paths
- Post-process trajectories using external tools for kinetic modeling
- Generate high-quality figures showing conformational changes
Instead of exporting full structures at each step, you can extract just the atomic movement you care about, for a cleaner and more focused dataset or visualization.
Step-by-step guide
Once you’ve computed unbinding paths using the Ligand Path Finder, make sure to:
- Select one or more paths from the Results tab in the Ligand Path Finder app.
- Install the Export Along Paths app from SAMSON Connect if you haven’t already.
- Choose the atoms you’re interested in. You can select them in the Document View or Viewport. For example, to track a specific ligand atom or an active center residue.
- Launch the Export Along Paths app. The app allows you to export the coordinates of selected atoms along the chosen path(s) at each state.
- You can then save the output in a preferred format for analysis, such as CSV or molecular structure files.
Here is what the path results table might look like before selecting the path to export from:
Best practices
- Before exporting, make sure your path contains conformations of interest and has a manageable state count for your application.
- If you’re only interested in low-energy regions, inspect the path using the energy plot and restrict export to selected state intervals.
- Use the info in the Results tab to identify paths with minimal energy barriers or optimal characteristics for further study.
Bonus: Visualize trajectory in SAMSON
After exporting, you can reimport atomic paths as trajectories in SAMSON to create visuals or animations, and even combine them with pathline visualizations (see the Pathlines app).
To learn more and get started, check out the full tutorial on Ligand Path Finder in the SAMSON documentation: https://documentation.samson-connect.net/tutorials/ligand-path-finder/ligand-path-finder/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.