AMBER Archive (2006)

Subject: Re: AMBER: Zinc coordinating CYS

From: madhumalar_at_bii-sg.org
Date: Thu Jul 27 2006 - 19:37:12 CDT

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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