If you’ve tried to build molecular systems with multiple copies of the same protein and coarse-grain them for simulations, you know how small quirks—like repeating chain IDs or overlapping residue indices—can cause big problems later in topology creation or force-field generation.
This post explores a structured approach to creating multiple protein replicas with unique identifiers using the Martinize2 Extension in SAMSON. Whether you’re preparing systems for membrane-protein simulations or modeling crowding effects, learning how to avoid these clashes can save hours of frustrating debugging.
Protein Replicas: Why Unique Chains Matter
Creating multiple replicas of a protein model might sound simple—copy and paste, right? But unless each chain and residue is uniquely labeled, software like Martinize2 can struggle to interpret the system, leading to incorrect or failed topology generation. This can derail simulation efforts, especially in replicas-based workflows.
From Single Chain to Multiple Replicas
Let’s take the example of Ubiquitin (PDB: 1UBQ), and walk through creating multiple replicas manually in SAMSON. The process ensures your replicated system is clean and ready for coarse-graining.
1. Make Atoms Fully Visible
Visibility helps isolate the components to replicate. Toggle the structural model visibility using the checkbox in the document view:
This ensures all atoms are viewable. You should now see a full atomic structure:
2. Copy and Move Chains
Select the chain(s) of interest:
Use Ctrl/Cmd + C and then Ctrl/Cmd + V to copy-paste the chain. Then, use the move editor (shortcut K) to place the new replica:
Repeat until the desired number of replicas is reached. You can even copy and move multiple chains at once:
3. Ensure Unique Chain and Residue Identifiers
This step is critical. Without it, your replicas might share overlapping identifiers, confusing Martinize2.
- Renumber Residues: Right-click on the structural model → Structural model > Renumber residues and structural groups. Leave the start index as 1.
- Renumber Chain IDs: Again, right-click → Structural model > Renumber chain IDs, starting at 0.
- Rename Chains: Give each chain a unique name using F2 or the Inspector.
Ready for Martinize2
Once your replicas are properly positioned, uniquely numbered, and named, proceed to Martinize2. Each replica will be treated as an independent input model, enabling parallel coarse-graining and topology generation.
This process is especially useful when simulating assemblies or testing structural variations. Clean input means fewer modeling errors later.
To learn more about setting up multiple-replica CG models, check out the full documentation here: SAMSON’s Martinize2 Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.