When generating coarse-grained (CG) models for molecular simulations using Martinize2 in SAMSON, one common issue arises when your system contains multiple chains or replicas: overlapping residue and chain identifiers. This can lead to errors during topology generation, especially in .top or .itp files for GROMACS.
For example, if two protein chains share the same residue numbers or chain names, Martinize2 may interpret them as part of the same molecule, or worse — generate incompatible topologies. Fortunately, SAMSON provides a streamlined process for renumbering and renaming chains to avoid this headache.
Why Renumbering Matters
Generating multiple replicas of the same biomolecular system is common practice in biomolecular simulations. Whether you’re building a molecular crowded environment or setting up replicas for enhanced sampling, ensuring that each chain has unique identifiers is critical.
Before passing these structures to Martinize2, here’s how you can sanitize your systems in SAMSON:
Step-by-Step: Unique Residue and Chain Identifiers
- Renumber Residues
Right-click on the structural model in the Document view and select Structural model > Renumber residues and structural groups.
This action will open a dialog where the default starting ID is 1. Click OK to reassign fresh, unique residue numbers to all residues.
- Renumber Chain IDs
Again, right-click on the structural model and choose Structural model > Renumber chain IDs.
Accept the default chain ID start value and click OK.
- Rename Chains
You can rename individual chains by selecting them in the Document view and pressing F2, or right-click and choose Rename. Alternatively, use the Inspector for easier batch renaming.
When to Do This
These cleanup steps are especially important if you:
- Use the Molecular Box Builder
- Copy chains manually in SAMSON
- Import multi-chain structures from external sources
Once this is done, you can safely proceed to load your structure into Martinize2 and generate valid topologies and CG models without conflicts.
Final Tips
- Always save your prepared system to avoid redoing steps.
- If you encounter errors with topology generation, double-check chain and residue uniqueness.
- This renumbering workflow also helps for downstream systems like GROMACS or when using the system in simulations with multiple molecules.
For the complete workflow on using Martinize2 in SAMSON, including model creation, side-chain corrections, and topology export, visit the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.