MD simulation of a bridging His coordinated to two ZN atoms

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1

GROMACS version:2023

I am trying to perform a MD simulation with a bridging histidine that is completely deprotonated and coordinated with Zn atoms on its epsilon and delta N. How should I proceed with this His? There is not much information about the parameters for this type of residue; or should it be parametrized as an entire group (ZN-His-Zn). Any suggestions?

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  1. You can parametrize the entire residue.
  2. You can use restraints just to keep them bound.
  3. You can use a force field that allows non bonded coordinated metals.

The answer you chose will depend on your resources and purpose of the project.

3

Hi @opalomino! Thanks for your response.

I am studying an protein which catalitic site has 3 Zn atoms, and in between 2 Zn there is a histidine completely deprotonated. The forcefield that I am using is CHARMM36, but it automatically assigns histidine protonation. In this case, should I define this His as a new residue with its own parameters? If so how do I validate afterwards?

4

I am not sure if CHARMM has the deprotonated histidines. If not, you will have to define it as new residue, parametrized through QM calculations.

5

No, CHARMM does not have this kind of histidine. I guess it need its own parameters… I have searched in a couple of databases which define paramaters and topology for non-standard residues but did not found this type of His… How can I validate these calculations afterwards?