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

Fasciculin-1 (1FAS)

This 3-finger toxin structure is available at high resolution (1.9 Å) and has all its heavy atoms present in the PDB file. We'll use one of the PDB2PQR servers to add hydrogens to this protein and optimize their positions.

1. From the PDB2PQR server web page, enter 1FAS into the PDB ID field.
2. Choose whichever forcefield and naming schemes you prefer.
3. 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.
4. Hit the "Submit" button.

Once the calculations are complete, you should get a web page with a link to the new PQR file. You can download this PQR file and view it in your favorite molecular visualization package (e.g., VMD, PyMOL, or PMV). For comparison, you might download the the original PDB file and compare the PDB2PQR-generated structure with the original to see where hydrogens were placed.

Calmodulin-dependent protein kinase (1A06)

This kinase structure is available at somewhat lower (2.5 Å) resolution and is missing several sidechain atoms as well as portions of its sequence. We'll use this example to demonstrate how PDB2PQR can add missing sidechain atoms to an imcomplete structure but cannot fill in missing regions of the backbone. In particular, we'll use PDB2PQR to add/optimize hydrogens, reconstruct sidechains K53, N65, R140, E154, Q192, Y195, E221, N222, K225, E228, K232, and Q272 from model geometries, and assign parameters.

1. From the PDB2PQR server web page, enter 1A06 into the PDB ID field.
2. Choose whichever forcefield and naming schemes you prefer.
3. 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.
4. Hit the "Submit" button.

Once the calculations are complete, you should see a web page with a link to the new PQR file and warnings about incomplete and poorly-positioned portions of the PQR structure. In particular, PDB2PQR will complain about missing regions between K53 and E64 and between F163 and P182. PDB2PQR may also complain "Unable to debump VAL A 189", referring to bad contacts between V189 and other residues that it was unable to resolve. You can download the resulting PQR file and view it in your favorite molecular visualization package (e.g., VMD, PyMOL, or PMV). For comparison, you might download the the original PDB file and compare the PDB2PQR-generated structure with the original to see where hydrogens were placed.