From: Aditya Padhi (
Date: Tue Oct 25 2016 - 19:44:12 CDT

Dear VMD users,

I have done some simulations on a zinc finger protein in AMBER and prepared
the zinc ion and its coordination by Cys and His residues using the ZAFF
forcefield (

After successfully generating the coordinate and topology files, when I am
visualizing it in VMD, It looks like VMD is not recognizing the Zinc ions
as the name of ZN has been changed to ZN4 in the input PDB file used for
simulations. As I want to inspect the Zinc ion coordination and visualize
it, I was wondering if anyone has any idea how to resolve this issue?

Is there a way to make VMD recognize the Zinc ions or I have to do some
modifications in the .mdcrd or .prmtop files to be able to visualize the

If anyone can help me in this regard, it would be great.