I recommend "GaussianView" software to draw your desired structure. We could draw the atoms by considering bonding, dihedral angle , ... (follow YouTube tutorials/software documentation). Graphene structure is well-studied and also we could use nanotube builder as a sketch tool.
Second possibility is saving the vmd output in PDB format and modifying/converting it using GaussianView for Gaussian input file.
Third possibility comes with other softwares like Multiwfn, Molden, ... as alternatives for GaussianView.
Fourth possibility (Hardest one) is modifying the files by programming languages (e.g python, c++, ...) to mimic the input file structure.
Y. Yamada, H. Yasuda, K. Murota, M. Nakamura, T. Sodesawa, S. Sato, "Analysis of heat-treated graphite oxide by X-ray photoelectron spectroscopy", J. Mater. Sci. 48(23) (2013) 8171-8198.