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

[David van der Spoel]

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