Hi Diana
Bredenberg and Nilsson Int journal of Quantum Chem 83, 230-244 2001
This paper describes modeling of Zinc Sulfhydryl bonds in Zinc fingers
The zinc is tetrahedrally coordinated.
Hope it helps.
Alpay
Date: Fri, 09 Jun 2006 15:51:03 +0200
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: [gmx-users] Re: Parameters for metals bonds inside proteins
To: [EMAIL PROTECTED], Discussion list for GROMACS users
<gmx-users@gromacs.org>
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Diana Rodriguez Ortiz wrote:
> Hi,
>
> I thank you for your attention. I tried to use the mailing list but
something has changed in that web page and I
> did not figure out how to enter my query. The metal is Zn and it is in a
tetrahedral strucuture. It is not completely
> shielded from the environment.
>
> Thanks,
> Diana
>
>
> David van der Spoel <[EMAIL PROTECTED]> wrote:
> Diana Rodriguez Ortiz wrote:
>
>> Hi Mr. Spoel,
>>
>> I am working with a small protein (50 aminoacids) that has a metal
atom near its center. Where can I find the
>>parameters to be able to run a molecular dynamics of this protein? In
this one, the metal is tied to 4 sulfurs I will
>>run it with gromacs. Can you help me?
>>
>
> This is not simple, you will have to search the literature and/or
> perform quantum calculations to obtain charges. You do not give much
> details though. What metal? Is it tetrahedrally coordinated, i.e. is the
> metal shielded from the environment completely? In that case you can
> make chemical bonds using the specbond method.
>
> Please continue this discussion on the gromacs mailing list.
>
>
>>Cordiially,
>>Diana Rodriguez
>>Intern at RPI
>>
>>-------------------------------------------------------------
>> Antes ahora y siempre COLEGIO
>> University of Puerto Rico at Mayaguez
>> http://www.uprm.edu
>>-------------------------------------------------------------
>>
>
>
>
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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