first of all, Remove the culprit that is causing the problem, you don't want to carry on doing it. Are you absolutely sure damage was caused by the other fish.
You must also check your water conditions, ammonia, nitrite, nitrate and pH. Fin rot can be associated with poor water conditions. I think it would be a good idea to post some photographs as well.Could you also tell us your tank setup, the size of the aquarium and what sort of filtration you are using
we need to establish what your water conditions are ,medications don't always work very well when water conditions are poor.
Sorry for questions, just imagine ringing up the vet and asking him to diagnose a problem with your dog without him actually being able to examine it?