It is not clear to me how the problem you describe is related to your having a system with more than 100 000 atoms.

It looks like the file read-watbox.str that you are using lacks the initial part:
*FILENAME: read-watbox.str
*PURPOSE: read 216 water molecule coord; used in solvation scripts
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
read coor card resid
* This is a box of 216 3-site water molecules in the experimental
* geometry. It was constructed from an equilibrated
* configuration of TIP4P (4-site water model of Jorgenson)
* waters at 1 atm pressure and a density of 0.0334 molecules/A**-3.
* The box edgelength is 18.856 A. The minimum image periodic
* boundary energy for this configuration using the TIP4P
* potentials is -2150.6833 kcal/mol.
*

It is not supposed to edited.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden