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>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to