AMBER Archive (2006)

Subject: Re: AMBER: Zinc coordinating CYS

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Thu Jul 27 2006 - 23:00:45 CDT

Hi Madhu
thanks for the reply. I will use the CYM residue type. But do I create
the bond between Zn and S by using the 'bond' command? this would make
a proper bond between the atoms and then I would require all the
parameters like bond length and dihedral angle which I dont have? are
these parameters available in Parm99.dat? How do i create an
artificial bond?

thanks for ur help again.
Rgds,
Nitin
On 27/07/06, madhumalar_at_bii-sg.org <madhumalar_at_bii-sg.org> wrote:
> Hi Nitin,
> U have to make CYS as CYM, which coordinates with ZN. then u have to
> create artificial bonds bet Zn & S of Cys. Later u should also load the
> corresponding parameter files..
>
>
> Madhu
>
>
> > Dear amber users,
> > I have three cystines coordinating a zinc atom. When i load the
> > protein with the zinc atom, it adds hydrogen atoms to the sulphurs and
> > they break the coordination of the zinc atom by the sulphurs. I read
> > about it and saw that another Cys type "CYX" could be used for it. But
> > then i need to specify the bond between the sulphurs. So, I was
> > wondering
> >
> > 1) can CYX residue type be used to keep the coordination of zinc by
> > the sulphurs?
> >
> > 2) how do I go about doing that? Is there a tutorial available to
> > crosslink and coordinate zinc?
> >
> > thanks a lot in advance,
> > Rgds,
> > Nitin
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
$B&-(BI+I$B'*(B
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu