Run on a treadmill and wear good, comfortable shoes. Don't overdo running as it may cause serious damage.
For that matter, anything you overdo is bad...
I have had knee injury from running a lot (partially because I am overweight). So my doctor recommended me to do some cardio using the eleptical (which BTW is not so demanding on your knees).
I stopped running for about 6 months until I recovered fully. Now I run, but a very limited distance and know how much to push.
Listen to what your body says, don't push it to the limit.