[gmx-users] how can i restrain Zn ion during simulations

Justin Lemkul jalemkul at vt.edu
Wed Feb 14 14:14:34 CET 2018

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

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list