When working with complex molecular systems, identifying molecular fragments or structural groups with specific electrostatic properties can be a crucial step — whether you’re designing new molecules, setting up simulations, or analyzing charge distributions. This becomes especially relevant when you need to quickly locate chemically reactive components or quantify charged moieties across large systems. Fortunately, this process can be simplified using the partialCharge attribute in the Node Specification Language (NSL) of SAMSON.
Why Partial Charges Matter
Partial charges influence how molecules interact, especially in polar media or within biological contexts such as protein-ligand binding. Identifying groups with high positive or negative partial charges allows modelers to predict potential binding sites, charge-driven interactions, and guide solvent placement decisions.
Using NSL to Find Structural Groups by Partial Charge
In SAMSON, the structuralGroup.partialCharge attribute (short name: sg.pc) enables you to filter structural groups based on their total partial charge. This makes it easy to query, select, and act on specific molecular fragments within large models.
How to Use sg.pc
The syntax for using the partial charge attribute follows standard comparison syntax. Here are some ready-to-use examples:
sg.pc 1— selects structural groups with a total partial charge of exactly 1.sg.pc > 1.5— selects groups with a partial charge greater than 1.5.sg.pc 1.5:2.0— selects groups with partial charges ranging from 1.5 to 2.0.
Real-Life Example: Searching for Charged Ligands in a Complex
Suppose you’re modeling a protein-ligand complex and want to isolate ligands that exhibit a partial charge higher than 2. Rather than analyzing every individual atom or guessing based on visual cues, you can simply type:
|
1 |
sg.pc > 2 |
All matching structural groups will be selected, allowing you to inspect or modify them directly. This not only saves time but reduces human error during selection.
Combining with Other NSL Attributes
The power of SAMSON’s NSL lies in combining multiple attributes. For instance, to find all visible groups with high partial charges, use:
|
1 |
sg.pc > 2 and sg.v |
This will restrict the selection to visually present structural groups in your scene.
Conclusion
This simple yet powerful mechanism helps you streamline workflows, especially when working with thousands of atoms and complicated charge distributions. You can use the partialCharge attribute in combination with others (like numberOfAtoms or formalCharge) to tailor your selections to your simulation or analysis needs.
To learn more and explore other filtering options, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.