The following examples will help orient you in APBS/PDB2PQR. Before beginning, please make sure to support the APBS/PDB2PQR team by registering for an account.
Best use of examples
Work through the examples in order, which begin with simple processes and end with advanced instances.
- Assigning Titration States With Propka
- Basic PDB File Operations
- Ligand Parameterization
- Running APBS through the PDB2PQR Web Portal
- Binding Energies
- Parallel execution for large problems
- pKa Calculations
- Lysozyme pKa example for PDB2PQR 1.9
- Potentials of mean force
- Solvation energies
- The Born ion