I am performing a molecular dynamic simulation of some halogenated compounds and some proteins. I generated the topologies of the ligand using the CGENFF webserver. When I got to the ionization stage, I realized an error that said that (duplicate atom index in virtual_site3). When I searched, I realized that I needed to generate the topologies of the compounds using the CHARMM GUI and also download some scripts from the Mackarell lab.

I would like to know how this is done to obtain the topologies.