Dear all,<div><br></div><div>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.</div>
<div><br></div><div>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 <a href="http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_species">as stated here</a>. I also saw <a href="http://jcp.aip.org/resource/1/jcpsa6/v132/i20/p205101_s1?view=fulltext">this paper</a> 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.</div>
<div><br></div><div>Is it sufficient to just introduce simple harmonic distant restraints to keep Zn in place?</div><div><br></div><div>Any advice would be greatly appreciated.</div><div><br></div><div>Thank you,</div><div>
Tom</div><div><br></div><div>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.<br clear="all">
<br>--<br>Thomas D. Grant<br>Graduate Research Assistant<br>Hauptman-Woodward Medical Research Institute<br>700 Ellicott St.<br>Buffalo, NY 14203<br><br>
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