Re: [AMBER] Zinc ion visualization from Amber trajectory

From: Eiros Zamora, Juan <>
Date: Wed, 26 Oct 2016 11:37:34 +0000

If you know the Zn atom has been renamed to ZN4 you could try ‘resname ZN4’, or alternatively, ‘not protein’ (which will display all atoms that don’t belong to amino acid residues).
> On 26 Oct 2016, at 01:45, Aditya Padhi <> wrote:
> Dear AMBER 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
> Zinc?
> If anyone can help me in this regard, it would be great.
> Thanks,
> Aditya
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Oct 26 2016 - 05:00:02 PDT
Custom Search