When modeling molecular systems, identifying hydrogen bond donors and acceptors quickly and accurately is often crucial. Whether you’re preparing structures for docking, analyzing interactions in a protein-ligand complex, or filtering atoms for visualization, being able to specify which atoms participate in hydrogen bonding saves time and improves analysis quality.
The Node Specification Language (NSL) in SAMSON offers powerful and concise filters for rapidly selecting such atoms—without writing complex scripts. Here’s how you can make use of it.
Why it matters
Hydrogen bond donors and acceptors play a central role in molecular recognition processes such as protein binding, DNA pairing, and even small molecule solvation. Manual identification is time-consuming and error-prone, especially in large biomolecular systems.
Using NSL in SAMSON, you can instantly highlight or isolate these atoms with simple, readable expressions.
Definitions used by SAMSON
- Hydrogen Bond Donor: A non-hydrogen atom that donates a hydrogen capable of forming a hydrogen bond (e.g., –NH, –OH).
- Hydrogen Bond Acceptor: An atom (typically O, N, F) that can accept a hydrogen bond.
Filter expressions you can use
To match hydrogen bond acceptors:
|
1 |
a.hba |
This will match all atoms that are designated as hydrogen bond acceptors in your structure.
To match hydrogen bond donors:
|
1 |
a.hbd |
This will match all atoms that are donating hydrogens that participate in hydrogen bonds.
You can also combine filters using logical operations. For example:
|
1 |
a.hbd and a.e Nitrogen |
This selects donor atoms that are nitrogen, helping narrow your view when analyzing specific interactions.
Visual tips
After defining these filters, you can highlight matched atoms with different colors, extract them into new selections for focused analysis, or use them as constraints in dynamics or optimization workflows inside SAMSON.
Additional fine-tuning
If you want to go further, NSL allows inclusion of other atom properties. For example, suppose you want to find atoms that:
- Are hydrogen bond donors (
a.hbd) - Have partial charge greater than 0.5 (
a.pc > 0.5)
You could express this as:
|
1 |
a.hbd and a.pc > 0.5 |
This gives you fine control to screen and analyze atoms with specific chemical behavior based on your model’s physical annotations.
Bonus: Donor-borne hydrogens
Sometimes you might want to select the hydrogens themselves that are involved in hydrogen bonding. Simply use:
|
1 |
a.dbh |
This filter matches hydrogens that are carried by hydrogen bond donor atoms.
These concise expressions remove the need for running dedicated scripts or relying on manual annotations, making your daily modeling work smoother.
Learn more in the full documentation page at:
https://documentation.samson-connect.net/users/latest/nsl/atom/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.