VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Nov 01 2016 - 14:42:04 CDT

Can you just use “name ZN4”? Do you just mean the problem is that the “ions” macro isn’t catching it?

Best,
JC

> On Oct 25, 2016, at 8:44 PM, Aditya Padhi <adi.uoh_at_gmail.com> wrote:
>
> 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 (http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm <http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm>).
>
> 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