Just like proteins, you need to make  a PSF and a modified PDB for your DNA. I would advise against using the AutoPSF graphical interface in VMD. Instead, use the text interface of psfgen itself, either through VMD or with the executable 'psfgen' provided with NAMD, and include the following line in your code:

alias residue DC CYT

which will change DC.

For a detailed explanation on how to prepare DNA for NAMD, try looking at this tutorial:

http://bionano.physics.illinois.edu/tutorials/introduction-md-simulation-dna-protein-systems

(from the website of one of TCBG's collaborators). It's about performing Steered-MD on a protein-DNA complex, and includes a section on preparing PSF and PDB files for structures containing DNA molecules.

Ambertools is also a good way to prepare the files for NAMD and you can choose various force field for your DNA and water. The following link is a tutorial.

http://ambermd.org/tutorials/basic/tutorial1/