PQR is believed to be stand for “PDB, Qharge, and Radius”. This is essentially a munged PDB file which contains partial charges and electrostatic radii for every atom suitable for use with the Adaptive Poisson-Boltzmann Solver.

The problem with PQR format is that it does not typically include PDB chain or segment identifiers, and is thus greatly limited in its ability to represent large atomic systems while still maintaining a unique set of identifiers for every atom. Therefore, PQR format should be avoided for anything other than preparing and checking APBS input.