For proteins in water (or other solvent) the route is described above.
For other systemd (eg. pure liquids or mixtures) one needs:
The atomic coordinates, which can be generated by a variety of
interactive programs (eg. Quanta, Cerius, HyperChem).
Coordinate files can be exported in pdb-format and
converted to .gro format by
the editconf program:
editconf -f conf.pdb -o conf.gro
where conf.gro is the coordinatefile,
or converted back to pdb-format by
editconf -f conf.gro -o conf.pdb
where conf is a file with coordinates, and conf.pdb is the target file in .pdb format.
NOTE: Make sure that the graphics programs export
whole molecules instead of molecules that are cut in pieces
(due to the periodic boundary conditions)
If you have the coordinates of single molecules, you can also
build systems (pure liquids or mixtures) with
genbox.
In contrast, the program
genconf
produces the lattice of molecules with random displacements.
The topology you have to build yourself. Of course you can
include topologies of part of your system (eg. spc.itp,
decane.itp etc.)