Atma means Self, while karaka means Indicator. There are naturally two grahas that are called Atmakaraka in the chart. One is natural (naisargik) and another is temporal (chara). Natural Atmakaraka in each chart is Surya, while chara Atmakaraka in each chart is calculated in accordance with a placement of a Graha in a sign.
Sun is an indicator of dharma (Natural Law principle). It rules self, innate nature and intelligence. While Moon rules manas (mind), sun is an indicator of Atman (a transcendental Self) which is unborn and undying, beyond the relative field of existence.