CONFLEX Tutorials

Introduction

CONFLEX is a program that performs conformation searches, host-ligand coordination searches, and crystal structure searches of organic molecules based on molecular mechanics simulations. Additionally, the program can predict normal vibrations, thermodynamic quantity, ultraviolet and visible light absorption spectrum, circular dichroic spectrum, and NMR coupling constant which are taking into conformational distribution.
This manual explains the various functions of CONFLEX through practical caluclations using existing organic molecules.

Table of Contents

  1. How to execute CONFLEX
  2. Structure optimization and vibrational analysis
  3. AMBER force field calculation
  4. Customize force field parameters
  5. Conformation search
  6. Conformer clustering
  7. Host-Ligand coordination search
  8. Crystal structure optimization
  9. Crystal structure search
  10. Grouping of crystal structures
  11. Crystal surface analysis
  12. Solvation free energy calculation
  13. Calculation of water/octanol partition coefficient
  14. NMR coupling constant calculation
  15. CD/UV spectrum analysis
  16. Amino acid residue substitution function
  17. Dynamics simulation using the dynamic reaction coordinate (DRC) method
  18. Optimization and conformation search using Gaussian program