unanswered Parametrization for zinc ions in a metalloprotein (MARTINI 3)

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3 months 2 weeks ago #9483 by fmeireles
Dear MARTINI developers,

I am parametrizing (in MARTINI 3) two zinc ions coordinated by 6 residues and 2 water molecules in the active site of a metalloprotein (PDB ID: 3LVZ).

My current approach is based on the paper by van Eerden et al ( pubs.acs.org/doi/10.1021/acs.jpcb.6b06865 ): I am representing both zinc ions as a single bead of type SD and charge +3 (the total approximate charge of the active site) and I am positioning this bead in the geometric center of the original zinc ions; I've placed a harmonic potential between the zinc bead and all the coordinating beads (except the water) and a weaker harmonic potential between the zinc bead and other non-coordinating residues within 0.52 nm (twice the vdW radius of an R type bead). All of these beads were excluded from non-bonded interactions with the zinc.

I've performed a test simulation under these conditions and the system seems at least stable, although I've yet to perform atomistic simulations to compare with the MARTINI one. Does this approach sound plausible or would you recommend me some modifications or some reading material that I might have missed?

Thank you very much in advance for your attention.

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