When setting up coarse-grained molecular dynamics (MD) simulations, many researchers seek to model systems with multiple identical proteins—often for crowding effects, comparative studies, or simulations of assemblies. A common challenge that arises during this workflow is how to correctly prepare multiple replicas of a protein without ending up with problematic topologies. This blog post describes how to do this efficiently using Martinize2 in SAMSON.
One recurring issue is that if residues and chains across replicas are not uniquely numbered and named, Martinize2 may generate incorrect or unusable topologies. Let’s go through the steps needed to avoid these conflicts.
Why numbering matters
Topology generators like Martinize2 need to assign unique identifiers to every residue and chain in a system. When several chains have overlapping IDs or residue numbers, the generated .top and .itp files can include duplicated entries or erroneous constraints, leading to failed simulations in packages like GROMACS.
Renumbering in SAMSON
The good news: SAMSON provides a simple way to renumber residues and chains so that every replica becomes uniquely identifiable, which inhibits conflicts during topology generation.
Here is how to resolve numbering conflicts:
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Once you’ve created your protein replicas in a SAMSON document (e.g. by using copy-paste or the Molecular Box Builder), select the atomic model of the entire structure.
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Right-click on the structural model and choose:
Structural model > Renumber residues and structural groups.
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In the pop-up dialog, leave the default starting residue ID at 1 and click “OK”.
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Again, right-click on the model and choose:
Structural model > Renumber chain IDs.
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Accept the default chain ID starting at 0 and confirm.
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Optionally, rename the chains for clarity by pressing F2 on each or using the Inspector panel:
Small effort, big impact
Correct numbering might seem like a small detail, but it saves a considerable amount of time otherwise spent troubleshooting broken topologies or debugging MD input files. By ensuring every chain and residue is uniquely defined within your structure, you set the stage for successful coarse-graining and simulation preparation.
Once renumbering is complete, you can follow the usual pipeline to generate your MARTINI CG models with Martinize2 in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.