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.
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