When preparing systems for molecular simulations using coarse-grained (CG) models, researchers often face a common hurdle: how to efficiently replicate molecular structures—such as proteins—multiple times with unique chain and residue identifiers, all while keeping the system organized for tools like Martinize2 and GROMACS.
If you’re modeling systems such as crowded cytoplasmic environments or constructing molecular assemblies, creating multiple replicas of proteins is essential. However, doing so incorrectly may lead to duplicated chain names or conflicting residue IDs, which break topology generation.
Here’s a concise guide on how to properly generate and configure multiple replicas of a protein, using SAMSON and its Martinize2 Extension. The process is surprisingly intuitive, and ensures that the output is valid downstream. ✨
Step-by-Step: Prepare Multiple Protein Replicas
1. Make Sure the Structure is Fully Visible
Before duplication, toggle visibility of the model to ensure all atoms are displayed. This allows you to select exactly what you want.
2. Select and Duplicate Chains
Use Ctrl/Cmd + C and Ctrl/Cmd + V to copy and paste a selected chain. Each paste creates a structural duplicate, conveniently placed on top of the original.
3. Move the New Copy
To arrange the copies in space, activate the Global Move Editor (shortcut: K) and move the new chain to a different position.
You can repeat this operation to create a desired number of replicas. It’s also possible to move multiple copies simultaneously.
4. Renumber Residues and Chains
Once all replicas are in place, it’s crucial to renumber residues and chain IDs to avoid conflicts during CG topology generation.
Renumber residue IDs:
Renumber chain IDs:
Rename chains: This can be done either through the right-click rename menu or using the Inspector.
5. Ready for Coarse-Graining
When chain IDs and residue numbers are cleaned up, you can proceed directly to the Martinize2 topology generation process—even for systems with multiple protein copies.
Being able to replicate systems efficiently helps you model complex environments without spending hours on error corrections. Try it out with your favorite structure—such as Ubiquitin (PDB: 1UBQ)—and explore the possibilities for large-scale CG simulations.
To learn more, visit the full documentation:
https://documentation.samson-connect.net/tutorials/martinize2/martinize2/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.