Divalent ion parameters in gromacs?

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Hi all.

I’m looking at simulating a protein that has a zinc cofactor. I’m initially going to simulate it without inhibitors in a box of water, but removing the bidentate inhibitor that’s part of the PDB file means the zinc cofactor now has 4 bonds (rather than 6) and is 2+ charge. Are there parameters for divalent ions as such?

Or would an alternative be to create topology and coordinate files in LEaP (what I’m planning on) and adding water at that stage?

Sam

2

Most force fields indeed support common divalent ions like Mg2+ and Zn2+, however their representation in additive force fields is quite crude. There are no coordinate covalent bonds in most representations, either, but these can be imposed via restraints, or left unbiased (most of the attractions are too strong so the geometries are preserved, but sometimes can distort due to the inaccuracies in the model). You’ll have to see what is appropriate for your system and chosen parameter set.

3

I suppose I can try both restraining and unbiased methods to see the best. The alternative idea is that the protein in question naturally doesn’t have an inhibitor, rather there is a water molecule (ligand) within the zinc atoms coordination sphere. I wonder if you replaced the inhibitor with water ligand(s) such that the zinc was neutral and ran that in a solvated box, would that be the same as running the protein with Zn2+/no water ligand in a solvated box?

4

I don’t understand this. The zinc ion is always going to carry a +2 charge, irrespective of whether a ligand is present or if a water is subsequently bound upon removal of the ligand. This is the approximation the force field will make.

5

Ah yes, that’s correct. I just remembered it’s listed as Zn2+ in the PDB file.

Thank you for the help