Quickly Find Charged Groups in Your Molecular Models

When exploring large molecular systems in SAMSON, identifying charged structural groups can be a repetitive and time-consuming task. Whether you’re validating a simulation setup, preparing a biomolecular system, or quickly inspecting charged fragments, having an easy way to filter and focus on structural groups based on partial or formal charges can make your workflow smoother and more efficient.

This is where the structuralGroup attributes in the Node Specification Language (NSL) come into play. If you’ve never used sg.pc or sg.fc before, this short guide will help you get started and show how to rapidly identify charged substructures in your scenes.

What’s the difference between formal and partial charge?

In the context of SAMSON’s NSL:

• Formal charge (sg.fc) refers to an integer value often used in structural representations and input files.
• Partial charge (sg.pc) is usually derived from quantum calculations or force field parameterizations and stored as floats, capturing subtler charge distributions.

Depending on your task, one or the other may be more relevant. Fortunately, SAMSON allows querying both easily.

Filtering by charge in NSL

Here are some quick examples for filtering structural groups (i.e., sg) by charge:

⚡ Formal Charge

Matches structural groups with a total formal charge of +1.

Selects all structural groups with formal charges ranging from +6 to +8. Useful for quickly spotting outliers or very charged moieties.

🔌 Partial Charge

Matches structural groups with partial charge greater than 1.5.

Filters groups whose partial charge falls in a moderate range—handy for charge analysis or visualization.

Layer your filters

You can combine charge conditions with other structuralGroup attributes such as number of atoms or atomic composition. For instance:

This expression selects small charged fragments—useful for separating solvents or ligands from bulk material.

Use Case: Charge hotspot detection

If you’re analyzing a protein-ligand complex or synthetic polymer, knowing where the most highly charged groups are can influence how you approach solvation, pKa predictions, or electrostatics calculations. NSL queries allow you to highlight only the structural groups relevant to these situations, potentially saving hours of manual inspection.

Conclusion

The ability to filter structural groups based on electrical charge directly from NSL makes SAMSON a powerful platform for model curation and exploration. Whether you’re modeling electrolytes, charged biomolecules, or drug-like compounds, using sg.fc and sg.pc can help streamline how you find and interpret charged groups.

To learn more about structuralGroup attributes and explore additional use cases, visit the official documentation at this page.

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