When modeling complex molecular systems, knowing which parts of your structure carry a net charge is essential. Charged regions can determine interactions with solvents, ligands, and other biomolecules, and they often play a central role in binding and reactivity. But scanning large models manually looking for charged structural groups can be slow and error-prone.
Fortunately, SAMSON’s Node Specification Language (NSL) offers a straightforward way to identify structural groups based on attributes like formal charge and partial charge. In this post, we’ll explore how to search for these properties using NSL on structural groups, saving you time and bringing accuracy to your molecular screenings.
What are Structural Groups in SAMSON?
Structural groups in SAMSON refer to sets of atoms that represent logical units in your model—like residues, ligands, functionalized surfaces, or fragments. NSL lets you query these groups using a flexible syntax with attributes tied to chemical or visual properties.
Filtering by Formal Charge
To identify structural groups carrying a specific formal charge, you can use the sg.fc attribute:
sg.fc 1: selects structural groups with a formal charge equal to +1.sg.fc 6:8: selects groups with a formal charge in the 6 to 8 range.
This is particularly useful when looking for highly charged residues or fragments—something common in metalloproteins or synthetic receptor design.
Filtering by Partial Charge
Unlike formal charge, partial charge gives a more nuanced picture of charge distribution. In SAMSON, NSL lets you select groups using sg.pc:
sg.pc > 1.5: finds structural groups where the total partial charge is above 1.5.sg.pc 1.5:2.0: selects structural groups with partial charges between 1.5 and 2.0.
This is useful when working with quantum chemical calculations or studying electrostatic interactions, especially within active sites or near interfaces.
When Should You Use These Queries?
Here are some scenarios where this can become a powerful productivity boost:
- Protein-Ligand docking: Focus on ligand candidates with a net charge matching binding site characteristics.
- Synthetic design: Filter out neutral groups and concentrate on charged moieties for ion-exchange applications.
- Electrostatics analysis: Identify charged fragments to be included in potential maps or coarse-grained models.
A Simple Tip
Want to combine charge filters with size constraints? Just combine queries:
|
1 |
sg.fc > 0 and sg.nat < 50 |
This example finds small, positively charged structural groups in your model.
To learn more about how to use NSL for structural group queries, check the full NSL documentation at https://documentation.samson-connect.net/users/latest/nsl/structuralGroup/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.