[gmx-users] Zn Coordination

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 5 18:24:09 CEST 2012

Thomas Grant wrote:
> Dear all,
> I am relatively new to GROMACS and MD in general.  I have gone through 
> various GROMACS tutorials and successfully run a couple of my own 
> simulations but that are pretty simple, i.e. just single chain protein 
> with standard amino acids in SPC/E, not requiring much expert knowledge. 
>  I am now dealing with a more involved protein-RNA complex bound to ATP 
> and a Zn ion.  I saw that GROMACS recognizes both ZN and ATP among its 
> standard building blocks.
> My question regards the coordination of the Zn ion.  In my crystal 
> structure Zn is coordinated by three cysteines and a histidine residue 
> as is common among nucleic acid binding proteins and is usually, as in 
> my case, only structural and not involved in active site catalysis. 
>  Since Zn is already recognized by default in GROMACS, do I need to be 
> concerned about the specifics of the Zn coordination?  I read in another 
> thread that it may be quite advanced, possibly requiring some 
> parameterization as stated here 
> <http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_species>. 
>  I also saw this paper 
> <http://jcp.aip.org/resource/1/jcpsa6/v132/i20/p205101_s1?view=fulltext> that 
> discusses Zn coordination but am unsure if it necessarily pertains to my 
> case or if this information has already been incorporated into GROMACS. 
> I'm not particularly interested in the specifics of the Zn site, but in 
> a distant part of the structure, I just don't want to have some weird or 
> drastic effect of the Zn finger unfolding or something along those lines.
> Is it sufficient to just introduce simple harmonic distant restraints to 
> keep Zn in place?

For simply keeping the Zn ion in place, that is probably sufficient.

> Any advice would be greatly appreciated.
> Thank you,
> Tom
> P.S. I am using the AMBER ff99SB force field after reading up on the 
> advantages and disadvantages of those available to GROMACS relating to 
> protein-nucleic acid complexes.  Any advice on this would also be 
> appreciated.

Seems like a reasonable choice.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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