When setting up coarse-grained (CG) molecular dynamics simulations for systems containing multiple copies of the same protein—such as membrane assemblies or multimeric complexes—one common pain point is efficiently and correctly preparing these replicas. This involves not just duplicating the molecular structure, but ensuring each replica is uniquely identifiable to avoid issues in topology generation and subsequent simulations.
If you use the Martinize2 Extension in SAMSON, here’s a guided method to generate multiple CG-compatible replicas of the same protein structure. This article focuses on replicating a protein system, renumbering chains and residues, and ensuring everything is ready before converting to coarse-grained models using Martinize2. These steps are essential to streamline your system setup without spending unnecessary time on manual corrections later on.
Step 1: Make Sure the Protein Structure is Fully Visible
Before making copies, it’s helpful to confirm that all atoms are visible. In the SAMSON Document View, toggle the visibility checkbox of the structural model to make sure nothing is hidden.
This should reveal the full model:
Step 2: Create Replicas
Select the chain(s) you’d like to replicate in the document view:
Copy and paste using Ctrl/Cmd + C and Ctrl/Cmd + V. This will duplicate the chain at the same position.
Next, use one of the move editors (e.g., Global Move Editor, shortcut K) to position the copied structure in space:
You can copy and move multiple chains simultaneously if you prefer working in batches:
Step 3: Renumber and Rename
Once all replicas are positioned as desired, it’s important to assign unique residue and chain IDs to each one. Martinize2 relies on clearly defined identifiers, and any conflicts can cause errors in topology generation.
Renumber Residue IDs
Right-click on the structural model > Structural model > Renumber residues and structural groups.
Set the starting index to 1 and click OK.
Renumber Chain IDs
Right-click the structural model again > Structural model > Renumber chain IDs.
Set the starting index to 0 and confirm.
Ensure Unique Names
Manually rename chains to unique names. Click on each chain and press F2 or right-click and use the Rename option in the context menu.
Final Tip: Save Your System
Once all replicas are prepared and uniquely identified, save your model. You’re now ready to continue with the standard Martinize2 workflow to generate CG topologies for multi-protein systems.
This approach eliminates downstream errors and prepares a clean, simulation-ready protein assembly, speeding up MD workflows for multimeric systems.
To learn more, visit the full documentation page: Martinize2 Extension Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.