The nuclie have charges equal to the sum of their protons. In force fields, molecules are represented as a collection of fixed charged point masses. Assigning charges to these point masses is not a completely resolved issue. Charge assingment methodology differs from force field to force field. The Gromos87 charges are the simplest possible and are the most rational from the mentality of general chemistry.
Aliphatic carbons have charges of zero.
Carbonyl carbons and oxygens have slight charges which sum to zero. The force field itself is a heavy atom representation. There is a Gromos96 which will come out soon. I do not have information on it other than it exist. The MacKerrel et al.