Some third-party programs have difficulty reading files which contain lone pairs.
You can choose whether or not lone pairs are included on the docked poses when GOLD writes these out, by ticking or unticking the Save lone pairs tickbox on the Information in File tab under Output Options of the GOLD Setup window.
You cannot choose whether or not lone pairs are included on the protein: when GOLD writes this protein file out, it will contain any lone pairs for atoms in the defined active site. If you wish, you can remove these lone pairs on the protein by loading into Hermes the protein file which is output by GOLD alongside the docked poses. Once this structure is loaded in Hermes, you can edit it by choosing Edit Structure from the Edit menu, then in the resultant Edit Structure window by clicking on the Unknown Atoms button and finally clicking on the protein molecule in the Hermes 3D visualiser to remove all unknown atoms within it (and hence all lone pairs). You can then save this edited protein file, and read it alongside your GOLD docking solutions.