Can I take magnesium with amino acids together? Also, what vitamins and minerals should I not take with mg. Affecting absorption?

It should not. Magnesium might interfere with some medications but not Amino Acids absorption. Why would you need to take Amino Acid supplement? Is it better that you eat a balance diet with enough protein, which would give you plenty of amino acids? It is more natural and complete variety of Amino Acids including the essential ones. Only in severe food allergy that you need a complete Amino Acid diet.