When analyzing molecular systems, identifying atoms with high partial charges is often essential for understanding reactivity, electrostatic interactions, or molecular dynamics behavior. For example, atoms with partial charges above a certain threshold can be involved in crucial non-covalent interactions such as hydrogen bonds or ionic contacts. But how do you efficiently find those atoms at scale when you’re working in complex biomolecular or materials modeling systems?
In SAMSON, this task becomes straightforward with the Node Specification Language (NSL). If you’re modeling systems where electrostatics play a critical role, here’s how you can use partial charge criteria to select what really matters.
Using a.pc to Filter by Partial Charge
In NSL, the attribute a.pc (short for atom.partialCharge) allows you to filter atoms based on their assigned partial charges. Partial charges are floating point values that must have been previously computed or imported.
Examples of how to use it:
a.pc >= 1.3: Select atoms with a partial charge greater than or equal to 1.3a.pc 0.7:2.0: Select atoms with a partial charge between 0.7 and 2.0
In many electrostatic maps, atoms with partial charges above 1.0 tend to signify sites of significant charge accumulation (common in acidic hydrogens, metal cations, etc.). Identifying these atoms quickly via NSL enables better focus in visualization or analysis workflows.
Combining With Other Filters
Partial charge filters can be combined with additional atom properties to narrow down selections:
a.pc > 1.5 and a.s O: Oxygen atoms with high partial charges — often found in metal-coordination or hydrogen-bonding contexts.a.pc > 1.2 and a.inRing false: Atoms with high partial charge that are not in rings (useful for avoiding aromatic systems).
Visual Applications
Use the NSL queries in SAMSON’s selection interface or color atoms based on query results to visually highlight areas of high electrostatic potential. This is particularly helpful when designing molecules for binding-site interactions, studying charged ligands, or evaluating molecular conformations after energy minimizations.
Summary
The a.pc attribute in SAMSON’s NSL allows you to isolate atoms based on partial charge criteria quickly and flexibly. Whether you’re fine-tuning a force field, studying charged interfaces, or preparing detailed atomistic graphs for publication, filtering by a.pc can save time and help focus your work.
To learn more about all available atomic attributes in SAMSON, and how to use them in NSL queries, visit the full NSL atom documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.