[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
> 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,
> 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
Seems like a reasonable choice.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users