Export atom trajectories along paths

The Export Along Paths extension in SAMSON allows you to export atomic coordinates (for all or only selected atoms) along defined paths - useful for preparing input files for reaction coordinate studies, free energy calculations, or extracting movement data from ligand pathways.

Getting Started

1. Log into SAMSON Connect.
2. Visit the Export Along Paths Extension page and click Add.
3. Restart SAMSON - your extension will be ready to use.

Step 1 - Load the Sample System

Load the sample system:

1. Click Home > Download.
2. Paste https://www.samson-connect.net/documents/046f1acd-c799-40f6-8185-cb4847eff795 ().
3. Click Download.

This will load a document with this tutorial's sample from SAMSON Connect.

The sample document contains a structural model of Lactose permease (1PV7) with its ligand Thiodigalactosid (TDG) and the unbinding paths generated with Ligand Path Finder (see the Ligand Path Finder tutorial). In the Document View (1), you can see the protein under the name Protein_chain_A, the ligand under the name TDG, and two paths.

1. Interface menu > Document view or
   , : Ctrl+1,
   : Cmd+1

Note

Paths are SAMSON nodes that store atomic trajectories of a group of atoms. Double-clicking on a path in the Document view starts/stops moving atoms along the path.

For some applications, it is useful to export the coordinates of a subset of atoms along the path, for example, to generate a reaction coordinate. For example, once you have computed an extraction path for a ligand (and optimized this path with e.g. the parallel nudged elastic band method), you might want to export the coordinates of the ligand along the path in order to perform free energy calculations.

Step 2 - Open the Export Along Paths App

Open the Export Along Paths app via Home > Apps > All > Export Along Paths . You can also find it in the Find everything... (Shift+E).

Step 3 - Export atoms trajectories along a path

Option 1 - Export All Atoms

1. Select one or more paths in the Document view.
2. Choose export mode:

• All frames in a single PDB file
• Each frame as a separate PDB file

3. Click Export atoms along paths to PDB files.

You'll be prompted to select a destination folder and file prefix.

Optional: Expand the Advanced section to change frame export interval.

Option 2 - Export a Subset of Atoms

1. Expand the Advanced panel.
2. Select a subset (e.g., ligand TDG) in the Document view.

3. Click Add to define this as a model to export.

This adds a named model (i.e., a group of atoms) to the export list:

You can:

• Rename the model by double-clicking its name.
• Add multiple sets of atoms.
• Click Select/Unselect to highlight included atoms. Or use the context menu for the corresponding line.
• Use the Reset () button to redefine. Or use the context menu for the corresponding line.

You can rename the model (i.e. the set of atoms) by double-clicking on the corresponding line in the list of models. You can add more models via the same procedure.

When ready:

• Choose export format (single or multiple PDB files).
• Select the relevant path(s).
• Click Export atoms along paths to PDB files.

You'll be prompted to select a destination folder and file prefix.

Use Cases in Molecular Modeling

• Generate reaction coordinate files for free energy profiling.
• Export ligand exit/entry trajectories for enhanced sampling.
• Output intermediate states for visualization, etc.
• Track only specific atoms (e.g., ligand, binding site, backbone).

Need Help?

Have questions or feedback? Feel free to reach out via the Forum, via e-mail, via the Feedback button in SAMSON, or by directly discussing with us.