When setting up coarse-grained (CG) molecular dynamics simulations using the MARTINI force field, one recurring roadblock for molecular modelers is handling multiple replicas of the same protein. Whether you’re modeling crowded cellular environments or testing multimeric assemblies, creating multiple instances of the same structure can quickly lead to topology generation issues. These typically arise when chain or residue identifiers are not properly managed after replication.
The Martinize2 Extension in SAMSON streamlines MARTINI topology creation, but special care is required when working with replicated systems. Here’s a practical, visual walkthrough on how to manually create protein replicas in SAMSON, while ensuring that IDs and names are set correctly for seamless topology generation with Martinize2.
Why Unique IDs Matter
Martinize2 uses chain and residue identifiers to map molecular structures and generate the correct topology files (.top and .itp) for CG simulations. If two residues or chains share the same ID or name, confusion in topology generation is almost guaranteed, often resulting in cryptic errors.
How to Create and Prepare Protein Replicas
Step 1: Copying Chains
First, load your protein structure into SAMSON. To replicate it manually:
- Make all atoms visible by toggling the structural model’s checkbox visibility.
- Select the chain(s) you want to copy.
- Copy and paste using Ctrl/Cmd + C and then Ctrl/Cmd + V.
This duplicates the chain in place, resulting in overlapping structures.
Step 2: Moving Replicas
Select the newly copied chain and activate the move tool (e.g. K for Global Move). Drag the replica to a new position. Use snapping options if precise placement is required.
Step 3: Repeat as Needed
Repeat steps 1 and 2 until you’ve created the desired number of protein replicas. You can also select and move multiple chains together to speed things up.
Step 4: Renumber Residues and Chains
This step is critical. Even though visually distinct, your replicas may share internal identifiers. To avoid MARTINI topology conflicts:
- Renumber residue IDs by right-clicking the structural model and going to Structural Model > Renumber residues and structural groups.
- Renumber chain IDs via Structural Model > Renumber chain IDs.
- Rename chains to unique names using F2 in the document or the Inspector tool.
What’s Next?
Now that your system has clearly differentiated replicas, you can proceed with the Martinize2 topology generation just like you would for a single structure: set the model in the Martinize2 extension, choose your options, and export the CG files.
For more detailed steps and visual aids, visit the original documentation page: Martinize2 in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.