Avoid Topology Errors in Molecular Dynamics: Renumbering Chains and Residues for Martinize2

One of the most common but often underestimated sources of errors when preparing molecular systems for coarse-grained simulations is improper residue and chain numbering. This becomes especially important when working with multiple copies (or replicas) of a protein in a single system.

Whether you’re building a simulation box with multiple replicas using tools like Molecular Box Builder or manually duplicating structures in SAMSON, incorrect or non-unique residue and chain IDs can result in topology generation issues in downstream steps—particularly when using the Martinize2 extension to prepare systems for the MARTINI force field.

Why It Matters

Each protein replica must have its own unique set of residue IDs and chain identifiers. If any two chains or residues share the same name or number, Martinize2 might not be able to parse the system correctly, leading to errors in the generated topologies and failing simulations in GROMACS.

How to Fix It in SAMSON

The good news: if you’re using SAMSON, there’s an integrated way to clean this up quickly and safely.

1. Renumber Residue IDs

To make all residue IDs unique across multiple replicas:

  • Right-click the structural model in the Document View.
  • Choose Structural model > Renumber residues and structural groups.
  • In the dialog that appears, leave the default start value as 1 and click OK.

Renumber residue IDs

Renumber residue IDs, dialog

2. Renumber Chain IDs

To ensure each chain has a unique ID:

  • Right-click the structural model.
  • Select Structural model > Renumber chain IDs.
  • Keep the default start value 0 and confirm with OK.

Renumber chain IDs

Renumber chain IDs, dialog

3. Rename Chains for Clarity

You can go one step further by giving meaningful names to each chain:

  • In the Document View, select the chain and press F2 to rename it, or right-click and choose Rename.
  • You can also do this through the Inspector.

Rename chains in the document

Rename chains in the Inspector

Moving On

Once your system is properly renumbered and uniquely labeled, you can proceed with generating Coarse-Grained (CG) models using Martinize2 without encountering parsing or topology generation issues. For single- or multi-replica systems, the smooth operation now depends on these simple yet crucial preparation steps.

To learn more and follow the complete process, visit the official tutorial on Martinize2.

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

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