Islands in Aqua-Planet runs
To add a land mass extracted from a global model to an aqua-planet simulation (eg. saagc) first set the initial conditions file of the aqua-planet run to that of the global model (Start_dump for a N48 run) and make sure that runs. The aqua-planet's land-sea mask should prevent the land in the initial condition file from appearing in the simulation.
The soil and vegetation parameters can be extracted from the IC file, so they can be turned off in the reconfiguration by going to Atmosphere->Ancilliary->Climatologies in the UMUI, going to the soil and vegetation pages and setting not used. Note that there is a next button on the Soil page that you should go through.
You can then create new land-sea mask and orography ancil files by copying those from the IC file and turning land points into sea. Note that you cannot add land points that weren't in the original simulation. Add the new land-sea mask to the Other ancillary section of the UMUI and set the number of land points in Atmosphere->Model Resolution->Horizontal and you should be able to run the simulation.
If the simulation fails to run correctly ensure that new ancil files have been used for both the mask and orography and that no new land gridpoints have been created that don't exist in the IC file.