Appendix D - van der Waals radii

The van der Waals radii of the atoms used by SURFNET are as follows:-

C   Carbon        1.87            P   Phosphorus    1.90
Fe  Iron          1.10            S   Sulphur       1.85
H   Hydrogen      1.20            X   Other         1.50
N   Nitrogen      1.65            0   Zero radius   0.00
O   Oxygen        1.40                                          

where all the radii are given in Ångstroms.

Note that the special atom type 0 has zero radius and is useful in some applications.

For surface files of type S, individual radii can be defined for each atom in the input PDB file using the B-factor column. To make SURFNET use these values, put an asterisk * between the filename in column 1 and the S option in column 2 in the OUTPUT FILES section of the surfnet.par parameter file.