When creating coarse-grained models from protein structures using the MARTINI force field, researchers often need to simulate multiple replicas of the same protein. For example, building a molecular box of repeated protein units is a common setup in membrane protein modeling and aggregation studies. However, one recurring pain point trips up many users—inconsistent chain and residue identifiers across replicas can break topology generation or simulate incorrect system behavior.
Fortunately, SAMSON offers a streamlined path to prepare such systems while avoiding these issues. In this blog post, we walk through how to properly renumber chains and residues for multiple replicas so that you can generate reliable topologies with Martinize2.
Why Renumbering Is Necessary
When you copy protein chains manually to create replicas in SAMSON, the default behavior is to keep their original chain names and residue numbers. This can result in:
- Clashing residue IDs between different chains
- Duplicated chain IDs or names
- Incorrect coarse-grained mapping or GROMACS errors during topology generation
To ensure each chain and residue is uniquely identifiable, a manual renumbering step is required—it only takes a minute and saves hours of debugging.
How to Renumber Chains and Residues
Once you’ve created your replicas (either manually or using the Molecular Box Builder), follow these steps in SAMSON:
1. Renumber Residue IDs
In the Document View:
- Right-click on the Structural Model that contains all your chains
- Select: Structural model > Renumber residues and structural groups
- Set the start value (e.g., 1) and confirm
2. Renumber Chain IDs
- Right-click on the same structural model
- Select: Structural model > Renumber chain IDs
- Leave the default value and click OK
3. Rename Chains with Unique Names
Go through all chains in the Document View:
- Click a chain, press F2, and type a new name (e.g., A, B, C…)
- Alternatively, use the Inspector panel to rename them
Wrap Up
Failing to correctly renumber chains and residues is among the most common sources of frustration when generating CG models for systems with multiple copies of the same protein. Luckily, SAMSON makes it visually intuitive and straightforward. Once you’ve completed the renumbering, proceed with generating the CG models via Martinize2 as you would for a single structure.
To learn more about creating coarse-grained models for the MARTINI force field using Martinize2, visit the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.