One common challenge in molecular modeling is capturing and comparing key conformational states during a simulation. Whether you are exploring structural flexibility, functional transitions, or designing ligands to fit various binding site shapes, keeping track of conformational changes is crucial. But how do you export or revisit these configurations efficiently?
Thankfully, the Normal Modes Advanced (NMA) extension in SAMSON offers a practical set of tools not only to generate flexible motions of molecular structures using nonlinear normal modes but also to save, store, and export conformations and trajectories in multiple useful formats.
Why saving conformations matters
Dynamic molecular models are at the core of understanding function. But without a mechanism to capture and compare specific states of motion, this dynamic information can be lost between simulation steps. With SAMSON, you can:
- Store significant structural conformations internally for fast recovery
- Create independent structural models based on intermediate states
- Export conformations and full trajectories to standard formats like PDB
Different ways to save structural snapshots
Let’s take a closer look at options available within the NMA module:
1. Store a conformation
You can store the current conformation directly into the SAMSON document (shortcut: S). This creates a reference state you can return to during your modeling session without re-computing the motion.
2. Create structural models
If you want to superimpose several states or use a structure independently from the motion module, the create button in the NMA module lets you embed the current structure as a separate SAMSON structural model. This is particularly helpful for comparing structural transitions or sharing specific molecular states with collaborators.
3. Export conformations and trajectories
You can export conformations (or entire trajectories) as standard PDB files. This is useful for downstream applications like docking, visualization, or analysis in other tools. Under the save frames tab, set a saving interval and use the export button to create the snapshot series.
4. Store the full motion as a trajectory
By clicking the Path button, you can save the entire motion as a trajectory node. This lets you replay and browse the motion in SAMSON at any time. Double-clicking the node plays or pauses the animation.
These tools help create a clear record of the dynamic behavior of the molecule, and facilitate comparisons, presentations, and downstream analyses.
To learn more, visit the full documentation page for the Normal Modes Advanced module: https://documentation.samson-connect.net/tutorials/nma/calculating-non-linear-normal-modes/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.