Creating Multiple Protein Replicas in SAMSON without Errors

Working on molecular simulations often means scaling up. Whether you’re modeling protein aggregation, crowded cellular environments, or simply running multiple replicas for statistical accuracy, duplicating protein structures is essential. But, if you’ve ever tried this manually, you’ve likely encountered issues with chain IDs, residue numbering, or incomplete topology generation when converting to coarse-grained (CG) models.

The Martinize2 SAMSON Extension simplifies the process of generating CG models, but what if your system includes multiple replicas of the same protein? Here’s a focused guide on how to create clean, valid replicas of proteins using SAMSON, without breaking your topology files downstream. 🧬

Why unique ID and chain names matter

When generating CG topologies (e.g. for GROMACS), each atom, residue, and chain must have a unique identifier. If residues or chains share IDs across replicas, the downstream tools may misinterpret the input, leading to invalid or nonfunctional topologies. This is especially critical when exporting to formats like .itp or .top.

Manually creating protein replicas in SAMSON

  1. Toggle visibility of the structural model to ensure all atoms are visible. This helps with accurate selection and placement.
  2. Select the chain(s) you want to replicate.
    Select chain(s)
  3. Copy and paste the chain(s) using Ctrl + C and Ctrl + V (or Cmd on macOS). This will create a replica at the same position.
    Copied chain
  4. Move the new chain using the global move editor. Shortcut: K. Turn on snapping for precise positioning.
    Create replica
  5. Repeat until you have as many replicas as you need.
    Create multiple replicas

Ensuring unique residue and chain identifiers

Once the replicas are in place, follow these steps to prevent downstream issues:

  1. Renumber residue IDs: Right-click the structural model → Structural model > Renumber residues and structural groups.
    Renumber residues
  2. In the dialog, set the starting number to 1 and click OK.
    Renumber residues dialog
  3. Renumber chain IDs: Right-click → Structural model > Renumber chain IDs, and set the starting index to 0.
    Renumber chain IDs
  4. Rename chains to human-readable names (e.g., A, B, C…) using F2 or the context menu.
    Rename chains

Best practices

  • Save your work regularly by exporting the system to a file.
  • Use the Inspector to quickly verify and modify chain IDs and names.
  • Once your replicas are clean, follow the steps in the Martinize2 tutorial to generate CG structures and topologies.

By ensuring your chains and residues are uniquely numbered and named, you can replicate systems safely and seamlessly integrate them into your molecular modeling workflow. This saves effort in debugging topologies and helps scale simulations for more realistic scenarios.

To explore detailed steps and see more examples, visit the full SAMSON Martinize2 tutorial.

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

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