Building a molecular system with several copies of the same protein can seem straightforward: duplicate a chain, move the copies apart, then generate a coarse-grained model. But there is a small bookkeeping step that can make a big difference. If replicas share residue identifiers or chain names, topology generation may run into problems.
This guide focuses on preparing multiple protein replicas for Martinize2 in SAMSON. The key idea is simple: keep the replicas together in one structural model, but make their residue numbering and chain identities unique before generating the coarse-grained structures and GROMACS topology files.
First, distinguish replicas from separate input models
Martinize2 treats each top-level structural model in the SAMSON document as a separate input. That means if you want several copies handled as replicas in one input, they need to be represented within the same structural model. If you select multiple structural models, Martinize2 generates separate coarse-grained models for them instead.
Before making copies, start with a clean atomistic structure. The tutorial recommends preparing the protein through Home > Prepare, removing items such as alternate locations, water, ions, ligands, and other crystallization molecules as appropriate for your system. For further guidance on cleaning and fixing structures, see the Protein Preparation & Validation tutorial.
Make copies and place them
You can create replicas with the Molecular Box Builder, a Python script, or manually in SAMSON. For the manual approach:
- Select the chain or chains you want to replicate.
- Copy and paste with Ctrl/Cmd + C, then Ctrl/Cmd + V. The copy is created in the same structure and position.
- With the new chain selected, use a move editor to reposition it. The Global Move Editor is available with the K shortcut.
- Repeat until you have the desired number of copies. You can also copy and move multiple chains at once.
At this stage, the copies may occupy the same coordinates or be positioned as you choose. The important preparation step comes next: assigning unique identifiers.
Give every replica distinct identifiers
Once the replicas are in place, make sure residue IDs are unique and chains have unique IDs and names. Otherwise, Martinize2 may encounter issues when creating topologies.
- Renumber residues: right-click the structural model and choose Structural model > Renumber residues and structural groups. The tutorial uses the default starting value of 1.
- Renumber chain IDs: right-click the structural model and choose Structural model > Renumber chain IDs. The tutorial leaves the default starting value of 0.
- Rename the chains: ensure the chains have unique names. You can rename a chain in the document with F2 or through the Inspector.
These are separate checks: renumbering residue IDs does not replace the need to make chain IDs and chain names unique. Once the identifiers are set, save the system so you can return to the prepared replica structure later.
Generate the coarse-grained models
Open Martinize2 from Home > Apps or through Find everything…, select the structural model in the document, and click Set. Review the options, including the force field and position-restraint choice, then choose a results folder and click Create coarse-grained models.
The output project includes an inputs folder, a log file, and an outputs folder. The outputs are organized by input model and include coarse-grained structures in PDB and GRO formats, GROMACS topology files such as .top and .itp, and a log containing Martinize2 command information. If the input is a single structural model, its generated coarse-grained model is loaded in SAMSON.
A useful workflow check is to confirm what you selected before running: one structural model containing uniquely identified replica chains is different from several top-level structural models, which Martinize2 processes separately.
For the full workflow and additional options, see the Martinize2 documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.