Hi Kyle,
The MMTK toolkit that Minimize uses does not have support for bromine currently.  Nonetheless there are some parameter files for bromine and iodine obtained from PyMOMO (http://www.pymomo.de/) that seem reasonable that, if you drop them into the right place in your Chimera distribution, should get your bromonaphthalene minimization to work.  For convenience, I've attached the files.  The "right place" is <your chimera installation>/lib/python2.7/site-packages/MMTK/Database/Atoms/ [on Windows or Linux] or Chimera.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MMTK/Database/Atoms/ [on Mac].
Hopefully MMTK will directly support these elements in future releases.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 30, 2012, at 12:10 AM, Kyle Morris wrote:

Hi,

I get a minimisation error - Atom type "Br" is not supported by MMTK - when trying to minimise a PDB that contains a bromonaphthalene covalently bound ligand. 

I have read the post by neelagiri.d at gmail.com  and note the Cl substitution does make this work but my Br is part of the molecule and so GAFF/Antechamber should be able to handle it I thought?