Using specbond.dat to define Zn-Cys bonds

Hi,
An alternative is to apply simple harmonic restrain between the two atoms (Zn and SG) : use [ bonds ] type 6 in the [ moleculetype ] section in the topology file.

See the following table for the synthax http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#topfile

Best regards
Alessandra