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

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 9 09:24:56 CEST 2006

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 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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