It's not a ligament that joins to the knee from the hamstrings. it would be a tendon. Your describing pain on the outside of your knees... It could be your ITB? this is a common sporting injury and can occur with beginning a new exercise regime, though it's not often associated with biking.
Other ways to loose weight that aren't as harsh on the joints (though biking really isn't) would be swimming. A brilliant exercise that makes you feel good.
To clarify exactly what the problem is invest in some physio - it's only recent pain and came on with starting exercise so it could be from your previous higher levels of activity but also could be something different and easy to fix with a bit of guidance.
Let us know how you get on.