Simplify Molecular Systems with Martinize2 in SAMSON

Coarse-graining (CG) is a powerful approach to simplify molecular systems, enabling faster simulations by reducing the complexity of all-atom models. If you’re a molecular modeler looking to apply the MARTINI force field, SAMSON’s Martinize2 Extension offers a streamlined workflow for creating CG models and topologies from atomistic structures. Let’s dive into how you can effectively use this tool!

Why Coarse-Graining Matters

Simulating large biological systems using all-atom models can be computationally intensive. Coarse-graining reduces this complexity by representing groups of atoms as single “beads.” For instance, an amino acid’s backbone is often modeled as a single bead. This simplification accelerates simulations, making it easier to study larger systems or run longer trajectories.

Creating Coarse-Grained Models: A Step-by-Step Guide

The Martinize2 Extension in SAMSON simplifies the process of generating CG models. Here’s how you can create a CG model using the example of the Ubiquitin protein (PDB code: 1UBQ):

  1. Load the Atomistic Structure: Start by loading the atomic structure of your protein into SAMSON. You can fetch structures directly from RCSB PDB via Home > Fetch. Just provide the PDB code and choose the format (e.g., PDB or PDB (mmCIF)).
  2. Prepare the System: Proper system preparation is crucial. Use Home > Prepare to remove alternate locations, water, ions, ligands, and other crystallization molecules. This ensures a clean input for Martinize2.
    Prepare a protein system
  3. Open Martinize2: Launch the Martinize2 application via Home > Apps or by searching it in Find everything…
  4. Select the Structural Model: Choose the atomistic structure in the document tree.
    Select the structural model in the document
  5. Set Options: Configure the Martinize2 options. For example, select the force field (e.g., martini3001), enable position restraints for specific beads (backbone, all, or none), and modify termini charges if desired.
    Martinize2 Options
  6. Set the Results Folder: Specify a folder where the output files will be generated. The results will automatically be saved in a timestamped project subfolder within this folder.
  7. Generate the CG Model: Click on Create coarse-grained models. You can monitor the progress in the log output. Once completed, the output includes PDB and GRO files of the CG model, topology files (.top and .itp) for GROMACS, and a log of the martinize2 command.

If you’re working on a single structure, the generated CG model can be directly loaded into SAMSON for visualization, where it appears as a collection of connected beads.
Created CG model

Benefits of the Streamlined Workflow

The Martinize2 Extension allows you to focus on your research rather than spending time managing technical nuances. By offering a seamless interface, automatic topology generation, and the integration of various options, you can create CG models tailored to your needs without hassle.

Whether you’re simulating a small protein or preparing a large biomolecular system, Martinize2 ensures accuracy and efficiency. And if you need to process multiple system replicas, SAMSON provides tools to create and manage such setups effortlessly.

For a more detailed guide, including creating replicas for systems with multiple protein copies or renumbering residues and chains, check out the full documentation here: https://documentation.samson-connect.net/tutorials/martinize2/martinize2/.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at https://www.samson-connect.net.

Comments are closed.