refinement of initial structure

Dear Modellers,

I have a manually constructed model and I would like to use the MODELLER optimisation protocol. I have attempted to follow the FAQ question 12, but I find that although MODELLER reads in the 'model.ini' file I give it, it then extracts restraints from the templates to refine the model.

Is there a way of presenting MODELLER with a model (minus any other details) and using the program purely as a structure refinement tool?

Any help would be appreciated,

Derek Smith