On 2/12/18 10:29 AM, vijayakumar gosu wrote:
Dear gromacs users,


I am currently running simulations for protein-RNA complex. However i have
to include one Zn ion which is coordinated by 4 cysteine residues. when i
performed energy minimization itself zinc displaces. How can i restrain to
Zn, or to freeze Zn during simulations.

Are you properly treating the Cys residues as anionic? If they're in the normal -SH state, I'd expect such a dissociation, but if they carry a -1 charge (as expected when coordinating Zn2+), I find that rather unusual.

You can enforce the coordination geometry with bonds, harmonic connections, or distance restraints. Check the manual for explanations.

-Justin

--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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