Creating Coarse-Grained Models for Multiple Protein Replicas in SAMSON

In many molecular simulations, especially when studying aggregation, crowding, or system size effects, researchers need to work with several replicas of the same protein. However, preparing these multi-replica systems for coarse-grained (CG) simulations can be a tedious and error-prone process—especially if done manually with traditional tools.

If you’ve ever tried to set up multiple copies of a protein for a MARTINI-based simulation, you probably encountered challenges like overlapping coordinates, duplicate residue or chain IDs, or difficulties generating consistent CG topologies. Fortunately, SAMSON—the integrative molecular design platform—offers a streamlined way to go from a single structure to a fully prepared CG model of a multi-replica system using the Martinize2 extension.

Why It Matters

When chains and residues are not uniquely numbered, topology generation using tools like Martinize2 can fail, or produce faulty models that complicate your simulation workflows. This blog post walks you through preparing a system of multiple protein replicas and generating their CG models using SAMSON—without needing to write any code.

1. Create Replicas of Your Protein

You can create protein replicas manually in SAMSON with just a few clicks. First, make sure all atoms are visible:

Toggle visibility

Then simply:

  1. Select the protein chain
  2. Copy (Ctrl+C / Cmd+C) and Paste (Ctrl+V / Cmd+V)
  3. Use the move editor (K) to reposition the new chain

Create replica

You can repeat this process to generate as many replicas as needed. Copying and moving multiple chains at once is also supported:

Create multiple replicas

2. Renumber Chains and Residues

Once you’ve created your replicas, make sure each residue has a unique ID and each chain has a unique name and ID. This is key for proper topology generation.

To renumber residue IDs:

  • Right-click on the structural model
  • Select Structural model > Renumber residues and structural groups

Renumber residues

Dialog

To renumber chain IDs:

  • Right-click the structural model
  • Select Structural model > Renumber chain IDs

Renumber chain IDs

Chain ID Dialog

Finally, rename each chain to ensure unique names. Use F2 in the document view or do this via the Inspector panel:

Inspector

3. Generate the Coarse-Grained Model

With all replicas created and uniquely identified, you can now proceed with CG model creation using Martinize2 just as you would with a single structure. Each structural model or chain will be treated separately, and the outputs (PDB, GRO, and topology files) will be automatically organized.

This approach reduces manual steps and helps avoid common issues that arise when preparing multi-copy systems for GROMACS simulations.

Learn More

If you’d like a detailed walkthrough, including setting Martinize2 options and generating topology files, visit the full tutorial at SAMSON’s Martinize2 documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.

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