Identifying Charged Atoms in Complex Molecules: A Quick Guide with NSL

When modeling molecules, identifying atoms with specific charges is vital in electrostatic interactions, pKa estimations, reactivity predictions, and more. Whether you’re building a molecular simulation from scratch or analyzing a protein-ligand complex, locating charged atoms quickly can save you hours of manual inspection 🧪.

Fortunately, the Node Specification Language (NSL) in SAMSON offers a straightforward way to find these atoms using attributes like formalCharge, oxidationState, and partialCharge. In this post, we walk through how to use NSL to highlight charged atoms efficiently, using syntax that makes your queries both precise and readable.

Understanding Charge Attributes

NSL provides three relevant atom attributes for charge-related queries:

• formalCharge (a.fc): Integer charge typically defined in molecular files.
• oxidationState (a.os): Common in coordination complexes or inorganic chemistry contexts.
• partialCharge (a.pc): Float value representing charge distribution in force fields.

Query Examples

Let’s say you want to find atoms with a positive formal charge. You can use the NSL query:

Need both positively and negatively charged atoms?

Looking for atoms with partial charges above a certain threshold, often relevant in polar regions?

For oxidation states, useful in transition metal complexes or redox-active molecules:

And if your simulation requires complex filtering, you can combine selections:

This returns oxygen atoms with negative formal charges—a scenario common in carboxylates or phosphates.

Combining Charge and Topological Filters

Need atoms that are both charged and located in a specific residue or chain?

This matches all atoms with non-zero charge in residues 45 through 60 of chain A.

Why Use NSL for This?

Many molecular modeling environments require plugins or manual selection to find charged atoms. NSL provides a readable, powerful grammar that works with attributes directly from your model. By using specific expressions, you can script structural inspections, automate selections, or feed commands into simulations—all without writing a single line of code beyond your selection itself.

Some Tips

• Use scientific units explicitly. NSL supports range queries (e.g. a.pc 0.5:1.0), which are invaluable in charge surfaces or QM selection contexts.
• Remember the short names. Instead of atom.partialCharge, just write a.pc—less typing, same result.
• Zero is still a value. If you’re filtering for neutral atoms, a.fc 0 works as expected.

Ready to try it out? Inside SAMSON, hit the NSL selection panel and experiment with these queries. You’ll quickly see how complex inspections can be reduced to a few characters.

Learn more in the full documentation.

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