lammps-users Digest, Vol 145, Issue 117

Juggling with the order of commands would be faster then asking here :rofl:

Your system sounds complex (graphene sheet, epoxy moleclues
surrounding it in a specific way). LAMMPS will not generally
build such a system exactly the way you want. That is a task
for a pre-processing build tool. There are several mentioned
on the LAMMPS website: Pre/Post processing link. They
output files in a format suitable for LAMMPS input.