Dear Esben, Gromacs can create pqr files, but does it in a very bad way - the radii information comes from a very limited set of atoms, and not directly from the forcefield parameters. A colleague of mine, Antonio Baptista, has written an awk script that can generate a proper pqr file from a gromacs topology - radii are computed from the non-bond interaction parameters for each type of atom.
Paulo
