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Contents

  • Modular Tutorials
    • ForceField Tutorials
      • Using LigandParam to Parameterize Ligands
      • FFPOPT Quick Start Guide - Installation
      • Linear Dihedral Scans with FFPOPT
      • Dihedral Scans using the WaveFront Method
      • Developing Custom Dihedral Parameters with FFPOPT
      • Divalent metal ion 12-6-4 models with Panteva–Giambasu–York (PGY) pairwise corrections for balanced interactions with nucleic acids
    • Alchemical Free Energy (AFE) Tutorials
    • Free Energy Surface Tutorials
    • Machine Learning Tutorials
    • Miscellaneous Tutorials
  • Workshop Materials
  • Internal guides
  • In Progress Tutorials
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ForceField Tutorials

Force Field Parameterization (Non-Standard Parameters)

  • Using LigandParam to Parameterize Ligands
    • Learning objectives
    • Relevant literature
    • Outline
    • Tutorial
      • Overview of Ligand Parameterization and Terminology
      • Parameterizing with LigandParam
  • FFPOPT Quick Start Guide - Installation
    • Learning objectives
    • Relevant literature
    • Tutorial
      • Installation
  • Linear Dihedral Scans with FFPOPT
    • Learning objectives
    • Relevant literature
    • Tutorial
      • Linear Dihedral Scans
  • Dihedral Scans using the WaveFront Method
    • Learning objectives
    • Relevant literature
    • Tutorial
      • WaveFront Dihedral Scans
  • Developing Custom Dihedral Parameters with FFPOPT
    • Learning objectives
    • Relevant literature
    • Tutorial
      • Dihedral Fitting
  • Divalent metal ion 12-6-4 models with Panteva–Giambasu–York (PGY) pairwise corrections for balanced interactions with nucleic acids
    • Learning objectives
    • Relevant literature
    • Introduction
      • The need to model ions–nucleic acids interactions
      • Limitations in modelling ions–nucleic interactions
      • How to overcome these limitations?
    • Tutoriel
      • Downloadable files
      • Building the topology with 12-6-4 parameters
      • Applying the PGY pairwise corrections
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