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

[Justin Lemkul]

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.
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Virginia Tech Department of Biochemistry

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