ZINK in Protein

User discussions
1

Dear all,
i have a protein, which is a dimer, and in each monomer there is a zink surrounded by 3 CYS and one HIS. i want to do md simulation, and i just want to keep it inside the protein. (at this point, i don’t need the ff parameter of zink, and i just want to keep it fixed inside the protein). i tried to add these lines at the end of my topol.top file:
[ intermolecular_interactions ]
[ distance_restraints ]
;ai aj type index type’ low up1 up2 fac
2197 1237 1 0 1 0.0 0.22 0.25 1.0
2197 869 1 0 1 0.0 0.22 0.25 1.0
2197 818 1 0 1 0.0 0.22 0.25 1.0
2197 1135 1 0 1 0.0 0.22 0.25 1.0

but still, zink escape from its position. what do you think i can do to fix this issue?

2

Have you enabled the usage of distance restraints in the md.mdp file?

3

You are absolutely right. I’d forgotten to activate the responsible parts in md.mdp. Thank you!

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4

While I understand that you do not wish to bother yourselves with the ff parameters for zinc, yet I feel that simulating proteins that have a zinc center is much easier using the Zinc AMBER force field (ZAFF). The exact workflow and structure preparation can be found here.

I used to manually add harmonic restraints just like you did, but encountered abrupt shifts in bond energy, which is why I shifted to using ZAFF. Might as well help you!

5

Thank you for your suggestion. I agree with you. Actually my protein is a homodimer with two ZINK in each monomer. I could use ZAFF successfully for a monomer, but for the dimer, I got some errors which I couldn’t solve. Since that part of protein was not so important, i skipped using ZAFF.
But, I think you’re absolutely right. It’s better that I put time to solve the issue and have a more accurate calculation!

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