Tutorials

This page contains several examples of how martinize2 can be used to convert proteins from atomistic to a martini3 representation.

You can find further examples on how to use martinize2 in the martinize-examples repository: https://github.com/marrink-lab/martinize-examples

• Basic usage
  • Overly basic usage
  • Minimal physical reality usage
    • Let martinize2 deal with secondary structure for you
    • User knows best
  • Other basic features of martinize2
    • Side chain fixing
    • Secondary and tertiary structure considerations
    • Cysteine bridges
    • Molecule naming
    • Citations
• Elastic Networks
  • Basic usage
  • Customising cutoffs
  • Using decays
  • Combining parameters
  • Defining structural units
  • Visualising elastic networks
• Gō models
  • Multiple Gō models in the same system
  • Note on multiple Gō models
  • Visualising Gō networks
• Water biasing
  • Water biasing for secondary structure
  • Water biasing for intrinsically disordered regions/proteins
• Mutations and modifications
  • General syntax
  • Mutate a single residue
  • Mutate all residues
• Adding new residues and links
  • The input force field
  • The output force field
  • The mapping
  • The Links
    • Links and Modifications
• Adding new modifications
  • The input force field
  • The output force field
  • The mapping