[gmx-users] RE: Re: Parameters for metals bonds inside proteins

Alpay Temiz temiz+ at pitt.edu
Fri Jun 9 16:39:24 CEST 2006

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. 

Date: Fri, 09 Jun 2006 15:51:03 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: [gmx-users] Re: Parameters for metals bonds inside proteins
To: dro22476 at uprm.edu,	Discussion list for GROMACS users
	<gmx-users at gromacs.org>
Message-ID: <44897CC7.1060509 at xray.bmc.uu.se>
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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 <spoel at xray.bmc.uu.se> 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.
>>Diana Rodriguez
>>Intern at RPI
>>	Antes ahora y siempre COLEGIO
>>	University of Puerto Rico at Mayaguez
>>	http://www.uprm.edu

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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