This is a common misconception. The fee is not based on the transferred value, it's only dependant on the size of the transaction (in bytes).
The size of the transaction only depends on the number of inputs and outputs, not their value.

Manually calculating a fee is something that's better left to more experienced users (imho), i'd suggest picking a good, decent wallet and following it's advice regarding fees. If you have no clue about inputs and outputs, don't try to pick your own fee, cause you'll end up in the situation where you payed 0.005 BTC as a fee for a 0.05 BTC transaction, and honestly believe the fee *has* to be sufficient... But that's not how it works i'm afraid...