[gmx-users] how can i restrain Zn ion during simulations
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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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