Ligand Preparation

• Check for Partial Charges

• Charging
  • Assign Partial Charges
  • Assign am1bcc partial charges
  • Assign mmff partial charges
  • Ligand Charges
  • Tautomer Normalization
  • pKa Normalization
• OMEGA
  • Build conformer using Distance Geometry
  • Enumerate Stereo Centers
  • Flipper
  • Generate 3D
  • Macrocycle Convergence
  • Omega Conformation
  • Omega Conformation (FastROCS mode)
  • Omega Conformation (Modes)
  • Omega Conformation (ROCS mode)
  • Omega Conformation (dense mode)
  • Omega Conformation (pose mode)
  • Omega Initial Conformation
  • Omega Macrocycle
  • Slice Ensemble
• Quacpac-prep
  • Reasonable Protomer
  • Remove Formal Charge
• ROCS-prep
  • Color Atom Coordinates
  • Compress Color Atoms
  • Count Color Atoms
  • Has Color Atoms
  • Has Compressed Color Atoms
  • Orient Grid By MOI
  • Orient Molecule By MOI
  • ROCS DB Prep
  • Remove Color Atoms
  • Uncompress Color Atoms
• Szybki
  • Fixed-Protein Ligand Minimization Individual
  • Fixed-Protein Ligand Minimization Series
  • Flex-Protein Ligand Energy
  • Flex-Protein Ligand Minimization
  • MMPBSA (Individual)
  • MMPBSA (Series)
  • Protein Ligand Energy Individual
  • Protein Ligand Energy Series
• Zap
  • Zap Ligand Prep
  • Zap Ligand Prep