Exporting Ligand Movement Along a Path in SAMSON

When studying molecular interactions, especially the dynamics of ligand binding and unbinding, one common challenge faced by computational chemists and modelers is the need to extract atomic coordinates along specific paths of motion. This data is crucial for generating reaction coordinates, performing free energy calculations, or visualizing intermediate states. Fortunately, the Export Along Paths extension in SAMSON provides an intuitive way to export these coordinates either for all atoms or selectively for specific molecular fragments.

In this blog post, we’ll explore how to export the coordinates of a subset of atoms (e.g., a ligand) along a predefined path using SAMSON. This operation is especially useful when you want to isolate the movement of a ligand from the rest of the system, which comes in handy for enhanced sampling, free energy profiling, or preparing input files for further simulation steps.

Step-by-step: Exporting a Subset of Atoms

You’ll first need to load a sample system from the SAMSON Connect library. Here, we’ll use a structural model of Lactose permease (PDB ID: 1PV7) with its ligand Thiodigalactosid (TDG) and two precomputed ligand unbinding paths. You can follow instructions from the documentation to download it directly into SAMSON.

Once the sample is opened, follow these steps:

  1. Open the Export Along Paths app via Home > Apps > All > Export Along Paths.
  2. Expand the Advanced panel in the app interface.
  3. In the Document view, select the ligand TDG. You can click on it directly in the scene or through the list of elements in the document view.

Select molecule in the Document view

  1. Click Add to define TDG as a model to export. This saves the selected set of atoms and adds them to a table.

A table with a molecule to export

You can:

  • Rename the model by double-clicking its name in the table.
  • Add multiple subsets (e.g., TDG and key residues from the binding pocket).
  • Use Select/Unselect or right-click for more options.
  • Re-define selections using the Reset button (erase

Now that your subset is defined, the final steps are:

  • Choose the export format (a single PDB file for all frames, or one PDB per frame).
  • Select the path(s) from the Document view.
  • Click Export atoms along paths to PDB files.

You will be prompted to choose a destination folder and prefix for the output files. These PDB files can then be used for further analysis and visualization, or as input for downstream workflows like umbrella sampling in molecular dynamics packages.

This level of control—being able to export just the atoms you care about along a path—can save time, reduce data size, and help focus your analysis on the most relevant parts of your system.

To learn more and find a detailed walkthrough with additional options, visit the full documentation page: Export Atoms Trajectories Along Paths.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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