Sorry for necroposting on this, but it's been viewed over 1,000 times so I figure people are still interested.
Anyhow, I think I came across a solution. I'm trying to do QM/MM calculations with uranium and was running into the same "Unrecognized potential number 6 in GetPot" error. I'm using the Stuttgart RSC 1997 basis set for uranium with a 60 core electron pseudopotential. My header included:
# opt oniom(b3lyp/gen:uff) nosymm scf=xqc int=grid=ultrafine pseudo=read
And at the bottom were included my basis sets and pseudopotential for uranium. After my jobs crashed a few times, I tried the following:
# opt oniom(b3lyp/genecp:uff) nosymm scf=xqc int=grid=ultrafine
You can see the changes were nothing too crazy. I simply indicated the use of pseudopotentials with the generic basis set and deleted the "pseudo=read" keyword. So far, so good.
Hope this helps.