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.bii-sg.org <madhumalar.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
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Received on Sun Jul 30 2006 - 06:07:11 PDT
