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. This charge and radius information can be provided to APBS in a few different formats which are described in more detail below. The section "Biomolecular structure formats" describes these formats in more detail.
The PQR format provides a very simple way to include parameter information by by replacing the occupancy and temperature columns of a PDB-format structure file with charge ("Q") and radius ("R") information. Unfortunately, the simplicity of this format also limits its extensibility: it can be very difficult to add new atom types and parameters in a generic format without the use of external software such as PDB2PQR. The XML parameter format described below is much easier to modify.
The XML structure format provides a somewhat more complicated format for including parameter information with increased flexibility in formatting, extension, and other modifications. As in the PQR format, atom coordinates are supplemented with charge and radius information. Please see the APBS user guide for complete format specifications.
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.
PDB2PQR will also perform hydrogen bond optimization, sidechain rotamer search, limited titration state assignment, ligand parameterization, and APBS input file preparation. Please see the PDB2PQR website for more details.
As mentioned above, PDB2PQR is discussed in more detailed on the PDB2PQR homepage. Therefore, we will review the minimal steps required to produce a PQR file from a PDB file here. To begin, choose a server from Downloads and web servers.
Start by choosing a PDB file to process. Either enter the 4-character PDB ID into PDB2PQR or accession number (e.g., 1FAS, 1MAH, 1LYS, etc.) or upload your own PDB file. Note that, if you choose to enter a 4-character PDB ID, PDB2PQR will process all recognizable chains of PDB file as it was deposited in the PDB (e.g., not the biological unit, any related transformations, etc.).
For most applications, the choice is easy: PARSE. This forcefield has been optimized for implicit solvent calculation and is probably the best choice for visualization of protein electrostatics and many common types of energetic calculations for proteins. However, AMBER and CHARMM may be more appropriate if you are attempting to compare directly to simulations performed with those force fields, require nucleic acid support, are simulating ligands parameterized with those force fields, etc.
It is also possible to upload a user-defined forcefield (e.g., to define radii and charges for ligands or unusual residues). Please see the PDB2PQR documentation for more information.
This is largely irrelevant to electrostatics calculations but may be important for visualization. When in doubt, choose the "Internal naming scheme" which attempts to conform to IUPAC standards.
These options fall into two categories: how to build missing atoms (including hydrogens) onto the structure and additional output configuration. Please see the PDB2PQR User Guide for more details.