Getting started — APBS-PDB2PQR 1.6 documentation

# Getting started

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.

## Using PDB2PQR to prepare structures

This section outlines the basic process of adding hydrogens and assigning charge/radius parameters to an otherwise complete PDB structure.

Fasciculin-1 is a 3-finger toxin structure available at reasonably high resolution (1.9 Å) and has all its heavy atoms present in the PDB file. We’ll use PDB2PQR to add hydrogens to this protein and optimize their positions.

- From the PDB2PQR server web page, enter `1FAS` into the PDB ID field.
- Choose whichever forcefield and naming schemes you prefer.
- Under options, be sure the “Ensure that new atoms are not rebuilt too close to existing atoms” and “Optimize the hydrogen bonding network” options are selected. You can select other options as well, if interested.
- Hit the “Submit” button.

From here, you can continue with APBS calculations on the server or download the file for other applications.

Note that lower-resolution structures such 1A06 may cause PDB2PQR to raise errors about missing segments of the protein that cannot be reconstructed. This behavior is expected.