If you’ve ever tried to generate a coarse-grained molecular model of a protein with multiple replicas, chances are you’ve run into errors related to chain or residue numbering. These issues, while common, can be frustrating — especially when you’re preparing input files for simulations with tools like GROMACS. This blog post focuses on one specific but crucial step in the modeling process: renumbering chains and residues to ensure error-free topology generation using Martinize2 in the SAMSON platform.
Why renumbering matters 🧬
When creating multiple copies (replicas) of the same protein in a structural model — for example, to simulate aggregation behavior or to build molecular boxes — it’s essential that each chain and residue is uniquely identified. Martinize2, which is used to generate coarse-grained (CG) models for the MARTINI force field, expects this. If there are duplicated IDs or names, it could produce incorrect topologies or fail entirely.
How to safely renumber residues and chains in SAMSON
Once you’ve created your protein replicas (manually or via a script), follow the three key renumbering steps to avoid clashes. Here’s how to do it:
- Renumber residue IDs: Right-click on the structural model and select Structural model > Renumber residues and structural groups.
Set the start index to 1 in the dialog and click OK:
- Renumber chain IDs: Again, right-click the structural model and select Structural model > Renumber chain IDs.
Leave the default setting (starting from 0) and click OK:
- Rename chains: Each chain should have a unique name. You can do this directly in the document panel by pressing F2 or using right-click > Rename.
Alternatively, rename chains in the Inspector panel:
Save your progress
Before moving on to generate your CG models via Martinize2, it’s good practice to save your system to a file. This ensures that your renumbering work is preserved and repeatable.
Who this helps
If you’re working on systems with multiple protein replicas—such as crowding simulations, vesicle construction, or protein condensation—this step is essential. It ensures that Martinize2 produces correct topologies and structures without manual debugging later in the pipeline.
Renumbering might seem trivial, but it’s one of those details that can make or break a molecular modeling project. It’s worth getting it right the first time.
To learn more about creating CG models with Martinize2 in SAMSON, including working with replicas, visit the full guide here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.