AMBER Archive (2006)

Subject: Re: AMBER: Zinc coordinating CYS

From: madhumalar_at_bii-sg.org
Date: Fri Jul 28 2006 - 04:17:36 CDT

Hi,
    Yes, U need to create artificial bond using bond command. Also, u need
to supply all the req parameters and it is not there in parm99.dat.
There is a very nice tutorial for treating metal ions, in the amber
tutorial section (by Ross Walker).
U can take parameters, from his thesis, which is also available..

http://www.rosswalker.co.uk/

Madhu

> 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
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