One common task in molecular modeling is to quickly identify and filter structures based on their electrostatic characteristics—namely, formal and partial charges. Whether you’re working with charged ligands, simulating ionized states, or preparing systems for docking and dynamics, locating structures with specific charges can be time-consuming. Fortunately, SAMSON provides powerful filters within its Node Specification Language (NSL) to handle this with precision.
In this blog post, we’ll focus on how to use structural model attributes in NSL to match molecules based on:
- Total formal charge (
sm.fc) - Total partial charge (
sm.pc)
⌁ Why charge matters
The electric charge of a molecule affects binding affinity, solvent interactions, and behavior in external fields. When analyzing molecular repositories, preparing simulations, or conducting experimental comparisons, filtering based on charge helps modelers narrow down viable models.
🔍 Formal Charge Filtering
To filter models with a specific formal charge, use the sm.fc attribute. For example:
sm.fc 1: Finds structures with total formal charge of +1.sm.fc 6:8: Finds all structures with total formal charge between +6 and +8.
This is efficient for spotting cationic or anionic structures in your system without manual inspection.
↯ Partial Charge Filtering
Partial charge captures electron distribution across the molecule. Use sm.pc to select structures based on their total partial charge. For example:
sm.pc > 1.5: All structures with partial charge greater than 1.5.sm.pc 1.5:2.0: All structures with partial charge in the 1.5–2.0 range.
This is especially helpful when preparing models for simulations that are sensitive to electrostatics (e.g., quantum mechanics, docking, or charge-dependent force-fields).
📋 Combine Conditions
You can combine both attributes to fine-tune selection. For example:
|
1 |
sm.fc 1 and sm.pc > 1.5 |
This selects models with formal charge +1 and partial charge exceeding 1.5—a frequent scenario when identifying protonated or highly polarized structures.
💡 Pro Tips
- Use wildcards along with name-based filters for more context (e.g.,
sm.n "acetate*" and sm.fc -1). - These queries can be saved and reused as filters within SAMSON’s Selection Editor or scripting workflows.
- Parameters like
sm.fcandsm.pcallow formatting ranges using colons (e.g.,6:10) and comparisons such as>,<.
Charge-based filtering is particularly useful when working with molecular databases, batch-processing structures for charge balancing, or managing large molecular systems. Instead of opening structures one by one or relying on external tools, SAMSON’s NSL lets you define charge-based queries directly in your workspace.
To learn more about all structural model attributes, visit the full documentation: https://documentation.samson-connect.net/users/latest/nsl/structuralModel/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.