SZYBKI

• Front Matter
• Installation and Platform Notes
  • Licenses
  • Installation
    • General Installation
    • Linux/Unix
    • Windows
    • Mac OS X
  • Uninstallation
    • Linux/Unix
    • Windows
    • Mac OS X
  • PVM
    • PVM hosts file
    • PVM Scaling
  • Open MPI
    • Using Open MPI
    • Open MPI License

SZYBKI Theory

• SZYBKI Theory
  • Force Field
    • Bond stretching
    • Angle bending
    • Stretch-bend interaction
    • Out-of-plane bending
    • Torsion interactions
    • Van der Waals interactions
    • Electrostatic interactions
  • Entropy evaluation
    • Configurational entropy
    • Solvation entropy
    • Protein-bound ligand entropy

Application

• Usage
  • Command Line Interface
    • Required Parameters
    • File Options
    • Potential Function Options
    • Optimization Options
    • Thermodynamics calculations options
    • PVM Options
• Examples of using SZYBKI
  • Free molecule optimization
    • Protein preparation
    • Ligand optimization in solution
    • Optimization with fixed atoms
  • Bound molecule optimization
    • Ligand optimization in the active site
  • Entropy calculation
    • Ligand entropy calculation in solution
    • Protein-bound Ligand entropy calculation
    • Binding entropy calculation
• Bibliography

Release Notes

• SZYBKI 1.7.0
• SZYBKI 1.5.1
• SZYBKI 1.5.0
• SZYBKI 1.3.4
• SZYBKI 1.3.3
• SZYBKI 1.3.2
• SZYBKI 1.3.1
• SZYBKI 1.3.0
• SZYBKI 1.2.2