If you’ve ever tried to predict ligand unbinding pathways from a deeply buried protein pocket, you’ve likely encountered a frustrating silence: no results, incomplete trajectories, or meandering paths in the wrong direction. One common, often overlooked reason? A poorly defined sampling box.
When using the Ligand Path Finder in SAMSON, correctly setting the sampling region is critical. This sampling box defines the search domain for the ligand’s active atoms and essentially dictates where the software is allowed to look for escape routes. If your ligand isn’t getting out, it may be because it’s not being allowed to.
Why Orientation Matters 🔄
The sampling box in Ligand Path Finder is defined in Cartesian coordinates. This means its position and volume are absolute, not relative to the protein’s shape or orientation. If your protein is rotated or offset, the sampling box may cover the wrong region, leaving potentially valid paths unexplored.
That’s why aligning the protein model appropriately beforehand is a core step. In the official tutorial, the example system is already aligned with the Z-axis to facilitate a clear unbinding route toward the periplasmic side.
Here’s an illustration of how the sampling box is defined and visualized:
Steps to Properly Define Your Sampling Region
- Make sure your system is appropriately oriented. Use the Move editors to rotate your structure or select specific atoms and align them with Cartesian axes by going to
Move selection > ...in the context menu. - Go to the Ligand Path Finder app and expand the Set the sampling region box.
- Adjust the box size and position based on the escape route you want to encourage. In the example case, an escape toward the periplasmic side is made easier by a box extended along the Z-direction.
- Verify your changes. A green box will be rendered in the viewport as visual confirmation of your sampling domain.
Tips You Shouldn’t Skip
- Avoid overly tight boxes. If the box is too small, pathways will be blocked early. If it’s too large, it may increase computation time.
- Visualize. Always confirm the green sampling box visually—it’s easier to spot issues this way.
- Use bounds strategically. If you know that certain directions are inaccessible (e.g., blocked by the membrane), you can bias the box away from them.
Here’s another view of how to define custom sampling dimensions directly in the app:
Not Just a Box—It’s a Hypothesis
Think of the sampling box as an expression of your hypothesis. If you believe that the ligand exits through a tunnel or known gateway region, you should align and expand your sampling region accordingly. This simple detail often makes the difference between productive and unproductive simulations.
To learn more, visit the complete Ligand Path Finder tutorial page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.