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 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


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