The Geneious Prime "Find restriction sites" tool can be used to find and annotate sites for nicking endonucleases (https://en.wikipedia.org/wiki/Nicking_enzyme).
Just import the attached .geneious file to create a list of nicking enzymes in Geneious. The enzymes included are Nb.BsaI, Nb.BspQI, Nb.BtsCI, Nb.SapI, Nt.BtsCI, Nt.SapI and V.Gel16401III.
You can set the list as the Candidate Enzymes: list in the Geneious Restriction Analysis Tab. Use the Advanced button to set the enzyme types you wish to detect.
The attached withrefm.just_nicks file is a text file example showing how these sites are defined in rebase format. This rebase file can also be imported into Geneious. Many thanks to REBASE for providing the list. Please cite the Restriction Enzyme Database if you use this list: See http://rebase.neb.com.