I forgot to mention that I think you can also construct the data file
for this system using a combination of Axel's nanotube and topotools
plugins for VMD. These scripts also has the optional ability to
create bonds (and angle/dihedral/improper interactions) connecting the
carbon atoms. (moltemplate does not do this for crystals.) The
tricky part is to figure out how to use topotools to delete the atoms
(and bonds, and angles, etc.) from the graphene wall where it
intersects the nanotube:
http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/
http://sites.google.com/site/akohlmey/software/topotools
Cheers
Andrew