That script was designed for a protein import, where most of the heavy atoms have coordinates, and won't work for a drug molecule with all coordinates unknown.
Check the topology file for the NAA residue to see if there is an IC table defined for that residue; if so, one can use commands like
IC SEED atom atom atom
If there is no IC table, you must provide one, either manually by editing the topology file, or via the IC GENERATE command (see intcor.doc). While the latter may be easier, it is known to have some issues, esp. with ring systems.