Separate table creation at runtime or add column
It is better to have single patient table.

Each doctor must have different UserId(or call PhysicianId) and then make entry in patient table with FkPhysicianId as a column and you can have one table for storing clinic information(auto incremented key can be used as ClinicId) and one for storing physicians Information like ClinicId etc. 

single patient table will be better as you don't need to add table for each practice you add and data can queried using joins on these table and maintaining too many table in future will be problomatic and other implementation in the EMR application as well.

I would suggest to have a Master Table to assign auto incremented Id to physician and patient as well.