Getting startedΒΆ

This section gives a basic overview of APBS-PDB2PQR workflows. It assumes that you have registered and obtained access to the software as described in How to get the software.

The basic APBS-PDB2PQR workflow involves a few simple steps, illustrated in the figure below and enumerated as:

  1. Identify your molecular structure for PDB2PQR by specifying a PDB ID or uploading your own structure.
  2. Use PDB2PQR to specify the titration state of the system, repair missing atoms, and assign parameters (charges and radii) to the atoms of your system.
  3. Run APBS from within PDB2PQR or via the command line.
  4. Visualize the results from within PDB2PQR or via Other software.
_images/APBS-and-PDB2PQR-user-flow.png