If you’re a molecular modeler, chances are you’ve encountered situations where you need to model multiple replicas of the same protein to simulate complex systems or processes. Ensuring each structure is consistent, correctly numbered, and easy to work with can be a challenge. With SAMSON, creating replicas manually for coarse-grained (CG) simulations, such as those used in the MARTINI force field, can be surprisingly simple. Here’s how.
Why Replicas Matter in Molecular Modeling
Replications in molecular modeling are essential for studying interactions between proteins, estimating ensemble properties, or building biological assemblies. However, manually creating these replicas often involves tedious steps, such as copying, moving, renumbering residues, and assigning unique chain IDs. SAMSON streamlines these tasks, making the process efficient and error-free.
Step-by-Step Guide to Creating Replicas
Here’s a streamlined method for manually creating replicas directly in SAMSON. We’ll use Ubiquitin (1UBQ), a commonly modeled protein, as an example.
1. Ensure All Atoms Are Visible
To begin, toggle the visibility of your structural model to ensure that all atoms are displayed. This makes selecting, copying, and placing structures easier.
This ensures you have a clear, fully visible structure to work with:
2. Copy and Paste Chains
Select the chain(s) you wish to replicate from the structural model. Use the simple copy-paste commands:
- Ctrl/Cmd + C to copy
- Ctrl/Cmd + V to paste
This creates a new copy of your chain(s) in the same position.
3. Move the Replica
After copying, move the new chain to its desired location using SAMSON’s move editors. Activate a move editor, such as the global move editor (shortcut: K), and reposition your replica.
Tip: Use translational and rotational snapping options in the top-left corner for precise positioning.
4. Create Multiple Replicas
Repeat the copy-paste and move steps until you have the desired number of replicas. You can even copy and move multiple chains at once!
5. Renumber Chains and Residues
To avoid issues in topology generation, ensure all residue and chain IDs across replicas are unique:
- Renumber residues: Right-click on the structural model and navigate to Structural model > Renumber residues and structural groups, setting the starting value to 1.
- Renumber chains: Right-click on the structural model and select Structural model > Renumber chain IDs, setting the starting value to 0.
- Rename chains: Rename chains either directly via F2, the context menu, or using the Inspector tool to ensure unique naming.
A Seamless Process
By following these steps, you can create, manage, and prepare CG-ready systems with multiple replicas in just a few clicks. From visibility toggling to unique numbering, SAMSON ensures accuracy and simplicity every step of the way. Whether for MARTINI force field modeling or other molecular dynamics tasks, this approach saves time while maintaining precision.
To dive deeper into coarse-grained modeling and learn more about SAMSON’s Martinize2 Extension, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today and simplify your molecular modeling workflows!