Ok, I understand. Ok, here I go:
Regarding the propeller twist, we can calculate this parameter even when the residue is modify. In my case, methylated cytosine. Since the methylation did not affect the atoms used to calculate the propeller twist, we can use 3DNA to calculate the propeller twist in this residue.
In the beginning I received the message of error because my methylated residue (cytosine) was named as DM in my pdb file. However, it seems that 3DNA just recognize the next names DA,DT,DC and DG. Then I just changed the name DM by DC in my pdb file and the software worked without problem. I hope it can be helpful for other persons.
Best,
Basilio.