cannot read from a data file(generated with Topotools)

Please keep the mail list in the loop.

Setting the box size correctly is fundamental

to your model, especially if it is periodic in
one or more dimensions. LAMMPS can’t guess
and do it for you (although you can relax the
box size later with an energy minmization or
constant pressure dynamics).

I suggest you read the read_data doc page carefully
and it’s discussion of how the specified box size
in the data file is used in conjunction with your
choice of boundaries (periodic, shrink-wrapped, fixed size, etc)
to map (or even lose) atom coords in the data file
into the simulation box.