Rigging mesh to skeleton using Milkshape 3D?

I have been trying to rig HL2 Citizen model to Half-Life 1 Scientist’s skeleton, but the model is always messed up when i try it out. What would be the right way of doing this?

Don’t use Milkshape, it’s terribly outdated. Use Blender instead (there are many, many tutorials for it on rigging and GoldSrc engine porting)