This format is a modification of the PDB format which allows users to add charge and radius parameters to existing PDB data while keeping it in a format amenable to visualization with standard molecular graphics programs. The origins of the PQR format are somewhat uncertain, but has been used by several computational biology software programs, including MEAD and AutoDock. UHBD uses a very similar format called QCD.
APBS reads very loosely-formatted PQR files: all fields are whitespace-delimited rather than the strict column formatting mandated by the PDB format. This more liberal formatting allows coordinates which are larger/smaller than ± 999 Å.
APBS reads data on a per-line basis from PQR files using the following format:
Field_name Atom_number Atom_name Residue_name Chain_ID Residue_number X Y Z Charge Radius
where the whitespace is the most important feature of this format. The fields are:
Clearly, this format can deviate wildly from PDB due to the use of whitespaces rather than specific column widths and alignments. This deviation can be particularly significant when large coordinate values are used. However, in order to maintain compatibility with most molecular graphics programs, the PDB2PQR program and the utilities provided with APBS (see the Parameterization section) attempt to preserve the PDB format as much as possible.