# APBS-PDB2PQR examples and tutorials

## PDB2PQR operations

In order to perform electrostatics calculations on your biomolecular structure of interest, you need to provide atomic charge and radius information to APBS. Charges are used to form the biomolecular charge distribution for the Poisson-Boltzmann (PB) equation while the radii are used to construct the dielectric and ionic accessibility functions.

The PDB2PQR web service and software will convert most PDB files into PQR format with some caveats. Although PDB2PQR can fix some missing heavy atoms in sidechains, it does not currently have the (nontrivial) capability to model in large regions of missing backbone and sidechain coordinates. Be patient and make certain that the job you submitted to the PDB2PQR website has finished and you have downloaded the resulting PQR file correctly. It usually takes less than 10 minutes for the job to finish.

This tutorial assumes that you have registered and have access to the PDB2PQR web server.

PDB2PQR examples

- Adding hydrogens and assigning parameters
- Parameterizing ligands

## APBS examples

APBS examples start with a PQR file (e.g., generated by PDB2PQR). Some of these examples can be performed through the PDB2PQR web interface but most require a command-line APBS program.

APBS examples

- Solvation energies with APBS
- Binding energies with APBS
- Protein-RNA binding linked equilibria
- Parallel APBS execution for large calculations

Todo

Migrate geoflow, pbsam, pbam examples over from `examples` directory.

## Visualizing results

There are several programs available for visualizing APBS results. The easiest is the PDB2PQR web server which provides 3Dmol.js <http://3dmol.csb.pitt.edu/> and Jmol <http://jmol.sourceforge.net/> browser-based visualization capabilities.

Other programs include:

- PyMOL
- VMD
- PMV
- Chimera

Visualization examples

- Using the PyMOL APBS plugin
  - Run the APBS calculation
  - Visualize the results
    - Electrostatic isocontours
    - Surface potentials
- Virtual reality with UnityMol

Todo

Add VMD tutorial.