Following on somewhat from this older post;

https://community.accelrys.com/message/9178#9178

While using the automatic charge group calculation, the groups made are very large, tending to be whole monomers.

Is there any way of modifying the setup to produce smaller groups like in the image posted by jdejoannis

Or is it going to be a case of drawing them manually / writing a script for scratch?

Thanks.