To be able to kill off the amoeba and other microorganisms in water you need to boil the water for up to 5 minutes.
After 5 minutes of boiling of the water the amoeba and any other microorganisms should be killed off in the water.
Then the water should be safe to drink as long as you boil it for a minimum of 5 minutes.
Boiling the water for 5 minutes can also get rid of some of the Chlorine that can be in city water but if you're drinking water from a stream or other source that is unknown as to how clean it is then boiling for 5 minutes can make the water safe to drink.
You can also buy some drinking water purification tablets that you drop into the water and it works to kill bacteria and microorganisms in the drinking water to make it safe to drink.