From: John Stone (
Date: Mon Feb 09 2015 - 15:28:59 CST

  Try using the atom type or element fields to assign the color
you want instead, I think that should circumvent this issue.

  John Stone

On Tue, Feb 03, 2015 at 09:56:20PM +0200, Debasish Mandal wrote:
> 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
> Debasish

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