Hi,
I have protein and ligand system with ZN+2 ion, but I am facing with stability of ligand and surrounding residues with zinc. I am using amber99sb-ildn.ff and ligand charges are produced using acpype gaff.
Recently I came accross a article in which they have talked about the highly charged metal ions parameterization using 12-6-4 LJ type nonbonded model.
Is it implementable in gromacs, if yes how it can be done.
Or is there other method through which I can resolve this problem.
It’s not yet included in Gromacs. Amber has it, and it can be done with OpenMM as well (if you read an Amber topology through Parmed). But I’m not sure if the Gromacs team is planning to implement it soon, perhaps Berk @hess can comment on that?
The only way we would support at 12-6-4 non-bonded potential would be through user supplied tabulated functions (which could maybe also be generated by writing the math formula). But we have not reintroduced those yet.
If there is a limited, or fixed, list of atoms pairs involved in these interactions, you can use user tabulated bonded interactions for these pairs.
Thanks, good to know for me as well.
BS"D
Martin Peters created a whole set of parameters for Zn bound to proteins:
Peters et al., (2010), Journal of Chemical Theory and Computation 6, p. 2935-2947.
I have a modified amber99sb-ildn FF for 2 Cys, 2His systems. What are your ligands for the Zn atoms?
Thank you for your response, I ll look into it.
I have 3 residues, HIS, ASP and GLU.
The ligand has an imadazole ring which is interacting with zn.
BS"D
I did that work quite some time ago, so I don’t remember all the details, but I did get two files from Martin that allowed me to use acpype to convert the necessary parameters into gromacs format, if you are interested. It was quite a lot of work to modify the force field, but the simulations were stable. Having the ligand as one of the Zn ligands makes things more complicated…