I am trying to develop parameters for AMBER FF and calculate Lennard-Jones parameters for Fe+3 ion. I really did a deep search and I found that it is the best way to use TDDFT for this with a high accuracy. I found many articles about this for example:
https://aip.scitation.org/doi/10.1063/1.2746031https://journals.aps.org/pra/abstract/10.1103/PhysRevA.78.032704 exc.. ( I can put more if there is need)
But, I couldn't understand articles because, in some articles there is so much mathematical formulas, in others method is not clear. So, to get clear things before starting, I need to get answer these: (Let's say I did my TDDFT calculation...)
1) After TDDFT calculations are there any software or tutorial to calculate vdw parameters ?
2) İf there is no any software or tutorial to calculate this, where can I start? Thank you
I'd bet there must be some LJ parameters available already for iron, which would be then a good starting point. I think the computational strategy would depend on several things What is the role of the ion? Is it a structural ion in e.g. an enzyme? Or rather a free cation in aqueous environment? What level of detail you require?
The Lennard-Jones potential should effectively represents non-covalent interactions other than charge-charge. In such a case, you may generate a dissociation curves of Fe3+ with some model molecules (e.g. peptides) at DFT and MM levels, and then fit the LJ parameters to match the DFT curves. Grimme's dispersion correction for DFT functionals contains C6 parameters for iron.
Solvent ions on the other hand were traditionally parametrized against macroscopic thermodynamic data, such as solvation free energies. Here I would start with reading papers, which report on the parametrization of Na+, Zn2+ and other ions.
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