When analyzing complex molecular systems, it’s common to face the challenge of identifying specific regions based on electrostatic properties. For instance, you may want to quickly locate highly charged structural groups that could be involved in salt bridges, ionic interactions, or reactive sites—especially in large protein assemblies, supramolecular complexes, or drug candidates. Doing this manually can be error-prone and time-consuming.
In SAMSON, the Node Specification Language (NSL) offers a flexible approach to querying complex molecular structures. When dealing with charged regions, the structuralGroup attribute space (short name: sg) introduces powerful filtering capabilities using formalCharge and partialCharge attributes. Let’s explore how to use these two attributes for efficient charge-based selection in SAMSON.
Formal Charges with sg.fc
The sg.fc attribute (short for structuralGroup.formalCharge) matches structural groups with specific total formal charge. Whether you’re looking for protonated amino acids or regions with a net negative charge, this attribute is ideal.
Examples:
sg.fc 1→ matches structural groups with a formal charge of +1.sg.fc 6:8→ matches structural groups whose formal charge is between +6 and +8—useful for identifying highly charged moieties in synthetic macrocycles.not sg.fc→ matches neutral structural groups with a formal charge of 0.
Partial Charges with sg.pc
Not all charge distribution insights come from formal charges. Especially in force field-based and semiempirical models, partial charges can reveal subtler electrostatic patterns across the system. Use sg.pc when you need to retrieve structural groups with specific partial charges.
Examples:
sg.pc > 1.5→ useful to find structural groups with significant positive polarity.sg.pc 1.5:2.0→ refines your selection to regions that have partial charges in this range.
Combining Charge Filters
Often, it’s helpful to combine both types of filters with logical operators to precisely target the parts of the molecule you care about. For example:
|
1 |
sg.fc > 0 and sg.pc > 1.2 |
This filter targets structural groups that have both a positive formal charge and a substantial positive partial charge—potentially highlighting protonated, electron-rich regions that may drive interactions in your system.
Understanding and utilizing these charge-based filters can help address common pain points in molecular modeling:
- ✅ Speed up the identification of charged functional groups.
- ✅ Locate charged residues in proteins more effectively.
- ✅ Quickly explore where counterions might be needed for system balancing in molecular simulations.
To dive deeper into all structural group attributes and examples, check out the full documentation page for NSL Structural Group: https://documentation.samson-connect.net/users/latest/nsl/structuralGroup/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.