Not against you, but he can press charges against your Mom if she does not have legal custody of you. But if you are in an abusive situation at your Dad's, the child services agency could place you with your Mom.
I'm sorry to hear that it sounds like things at your Dad's are not well. Divorce and separation, multiple houses etc can be a strain on anyone.
Before running away, is there an adult you trust in your family or close to your friendship circle who could help you and your Dad to work out some solutions to the problems?
Conflict between teens and parents is a natural and required part of growing independent. How you and your folks handle it sets the basis for your future adult relationship.
Other places which could help are your school counselors, church minister or social worker, local youth health organisation, some hospitals and health services have similar too.
If you feel in danger from your Dad, rather than really irritated, follow your instincts and go to a friend's / neighbour's house for support.
Contact child advocates in your area. From my understanding I wouldnt think so, but I could be wrong.
But above all if you feel yourself in danger, do not stop to think, call a family member you trust, the police if necessary.
http://www.boystown.org/ they are a good group and can help.