When modeling biomolecular systems at a coarse-grained (CG) level using the MARTINI force field, one common situation arises: scientists often want to simulate *multiple replicas of the same protein*, such as in crowded environments or assembly studies. However, preparing such systems can be tedious, especially when ensuring that structural identifiers remain unique. Misnumbered chains or residues can silently break topology generation and derail workflows later on.
The Martinize2 Extension in SAMSON, an integrative molecular design platform, offers a solution that is both visual and scriptable. In this post, we’ll walk through how to manually generate and properly prepare multiple replicas of a protein—for example, Ubiquitin (1UBQ)—so that they are ready for CG modeling using MARTINI.
Step-by-step: Creating and Preparing Replicas
1. Make atoms fully visible.
Toggle the visibility of the structural model (uncheck and check it in the document view). This ensures all atoms are shown, which helps when selecting and copying chains.
2. Select chain(s) to replicate.
Click on the chain of interest in the document view or in the viewport.
3. Copy and paste the chain.
Use Ctrl/Cmd + C and then Ctrl/Cmd + V to duplicate the chain. A new replica will appear in the exact same position.
4. Move the new replica.
Use the global move editor (shortcut K) to reposition the replica spatially.
You can repeat these steps to create more replicas. TIP: You can select and copy multiple chains at once to speed up the process.
Crucial Step: Renumber and Rename for Uniqueness
After creating all the desired replicas, the following adjustments are essential before proceeding to CG modeling:
- Renumber residue IDs so that each residue has a unique identifier across the model. Right-click the structural model > Renumber residues and structural groups.
- Renumber chain IDs to assign unique chain indices. Right-click the structural model > Renumber chain IDs.
- Rename chains (if needed) to avoid repeated names. Use F2 or right-click > Rename in the document view. Alternatively, use the Inspector panel for efficient bulk renaming.
What’s Next?
Once the system has been visually arranged and identifiers cleaned up, you’re ready to use the Martinize2 Extension to build coarse-grained models for each structure. For that, follow the standard procedure in the section Creating CG model from atomic structure.
Being able to visually manipulate and replicate protein structures directly within an integrative platform like SAMSON—with proper support for numbering, naming, and moving—is useful for building multimeric systems or simulating phenomena such as phase separation or aggregation.
To learn more, explore the full Martinize2 tutorial at the SAMSON documentation center: 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.