[gmx-users] Zn Coordination

Thomas Grant tgrant at hwi.buffalo.edu
Thu Apr 5 17:58:02 CEST 2012

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
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?

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

Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203
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