[lammps-users] difficulty using molecule command to add a molecule

You get the warning because your molecule file has per-atom masses, while your atom style full uses per-atomtype masses and thus the molecule file should not have a Masses section. The masses will be set by the data file or the mass command or both.

While you have added space for additional types, you also need to reserve space to actually store bonds and angles. In LAMMPS that information is stored with individual atoms. With newton bond on (the default) each bond, angle, dihedral or improper is stored by default with one of its constituent atoms. The read_data command will use the minimal amount suitable with the topology contained in the data file (for water molecules, those will be 2 bonds, 1 angle, and 2 special neighbors per atom). You get the error because your molecule file requires more space, most certainly more special neighbors.