From: Debasish Mandal (
Date: Tue Feb 03 2015 - 13:56:20 CST

Hello VMD users,
                                    I am working on the dynamics of protein
substrate complex. The substrate, a organic molecule, possess a chlorine
atom. I wants to prepare topology using VMD paratool but it is
not Recognizing Cl atom. could you please provide me any idea how to solve
it? In VMD window Cl atom shows the same color as of carbon atom. Please
let me know how to change it?

Your help will be greatly appreciated.

Thanks & Regards