When working with complex molecular systems, understanding how charge is distributed is often key to understanding behavior—especially in systems involving electrostatics, binding interactions, or solvation. One common challenge for molecular modelers is quickly identifying structural groups with specific partial charges. This is where the partialCharge attribute in SAMSON’s Node Specification Language (NSL) becomes useful.
SAMSON allows users to define and search within structural group nodes using this partialCharge attribute, which lets you filter groups based on their total partial charge. This can save time and help you generate more focused analysis or simulations.
Why care about partial charge?
Whether you’re setting up a molecular dynamics simulation or analyzing electrostatic potentials around a molecule, identifying charged regions is an essential step. Perhaps you’re preparing a system for a docking study and need to locate positively charged pockets, or maybe you’re trying to explain reactivity patterns in a system. Directly querying group-level partial charges instead of manually inspecting atoms can make this task easier.
Using sg.pc in practice
In NSL, the structuralGroup.partialCharge attribute, abbreviated as sg.pc, gives you access to the total partial charge of structural groups. You can specify exact values, inequalities, or even ranges to quickly narrow down your search.
Examples
sg.pc 1– finds structural groups with a total partial charge of exactly 1.sg.pc > 1.5– finds structural groups where the total partial charge is greater than 1.5.sg.pc 1.5:2.0– returns structural groups with partial charges between 1.5 and 2.0.
This is particularly useful when you’re working with large complexes and want to isolate regions of high or low partial charge to investigate their role in interactions or dynamics. For instance, you might ask:
- Are there any groups that have abnormally high local partial charge?
- Which parts of the molecule contribute most to the polarity?
When is this useful?
This feature is helpful in many contexts:
- Drug design: Identify potential binding hot-spots or highly charged pharmacophores.
- Molecular screening: Filter out candidates based on charge behavior within specific functional units.
- Electrostatic analysis: Map partial charge distributions and correlate with solvent accessibility.
The partialCharge attribute in SAMSON is not just a filter – it’s a lens that helps molecular modelers see their system in new ways, all without writing custom scripts or diving into manual selection processes.
To explore these functionalities in more detail, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.