Re: [AMBER] Zinc ion visualization from Amber trajectory

From: Aditya Padhi <adi.uoh.gmail.com>
Date: Thu, 27 Oct 2016 11:11:31 +0900

Hi Juan,

Thanks for your reply. In VMD, it doesn't even list the ZN4 in the sequence
viewer, however, it displays both protein and DNA that my system contains.
So, I was not able to use the resname or resid flag. Interestingly, when I
visualize the trajectory in Chimera, the Zinc ion coordination does show up!

However, I found that the problem was with the version of VMD. I can see
the ZN4 using resname flag in VMD 1.9.2, in earlier version however, it was
not showing up for some reason.

Thanks,
Aditya

On Wed, Oct 26, 2016 at 8:37 PM, Eiros Zamora, Juan <
j.eiros-zamora14.imperial.ac.uk> wrote:

> 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).
> Cheers
> Juan
> > On 26 Oct 2016, at 01:45, Aditya Padhi <adi.uoh.gmail.com> 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 (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
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-- 
*****************************************************
Aditya Kumar Padhi, PhD (IIT Delhi)
Postdoctoral Researcher,
RIKEN - Yokohama,
Japan
Contact no: 070-3999-2091
*****************************************************
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Received on Wed Oct 26 2016 - 19:30:03 PDT
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