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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>
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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
