I now understand what this means and corrected this error in the gro file. I now have an error in energy minimization. There is another thread with a similar error but I was wondering if there were additional suggestions, or if you had additional feedback on them.
The error is:
Energy minimization has stopped because the force on at least one atom is not finite. This usually means atoms are overlapping. Modify the input coordinates to remove atom overlap or use soft-core potentials with the free energy code to avoid infinite forces. You could also be lucky that switching to double precision is sufficient to obtain finite forces.
Writing lowest energy coordinates.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 500.
Potential Energy = 6.9141134e+18
Maximum force = inf on atom 98449
Norm of force = inf
No approaches received feedback from the other thread (posted below) and so I was wondering if there were additional suggestions to try.
Again, I greatly appreciate all of your guidance on this. It has been a great learning opportunity.