Creating coarse-grained (CG) models helps reduce simulation time and computational cost by simplifying atomistic structures. But what if you’re working on systems with multiple protein replicas—for example, repeated units in biological assemblies or membrane-embedded protein clusters?
This scenario is common but easy to get wrong. Overlapping residue or chain IDs among replicas can silently cause downstream issues in topology generation and molecular dynamics simulations using tools like GROMACS. Fortunately, the Martinize2 Extension in SAMSON offers a streamlined way to handle this, provided you follow a few key steps.
Why Unique Identifiers Matter
Each replica in your system must have its own unique chain and residue identifiers. Without this, topology generators like Martinize2 may fail or output incorrect structures—errors that often show up late in the process and are hard to debug.
How to Prepare Your Replica System Correctly
Here’s a practical workflow using SAMSON to generate well-prepared replicas:
1. Make All Atoms Visible
Before copying, ensure the full atomic structure is visible:
This will help you select, copy, and reposition atoms more intuitively.
2. Copy and Paste Chains
- Select the chain you want to duplicate.
- Use Ctrl+C, then Ctrl+V (or Cmd on Mac).
- With the new chain selected, switch to a move editor (e.g., global move editor, shortcut K) and reposition the replica.
You can repeat this step or copy multiple chains simultaneously if needed.
3. Renumber Residue and Chain IDs
This is crucial. In the document view:
- Right-click the structural model, then go to Structural model > Renumber residues and structural groups.
- In the dialog, leave the default start ID (1) and click OK.
- Repeat for chain IDs (Renumber chain IDs) with a start value of 0.
4. Rename Chains
To avoid name collisions, right-click each chain and select Rename or press F2:
You can also use the Inspector for bulk edits.
Good to Know
- The copied chains will initially appear at the same location—make sure to move them manually.
- You can enable snapping to position replicas with precision.
- Always save your project before processing with Martinize2 to preserve your setup.
Once these steps are done, you can proceed with generating your coarse-grained model using the same pipeline described in the atomic-to-CG model workflow.
These precautions save time and headaches later on, preventing subtle issues in simulations and making your CG models more reliable.
To learn more, visit the full documentation page: documentation.samson-connect.net/tutorials/martinize2/martinize2/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.