ricalessandri
commented
2 years ago Yep, some examples can be useful. I'll add this to my to-do list.
In the meantime, have a look at Supplementary Table 25 of the Supp. Info. of the Martini 3 main paper. The table reports default bead assignments for cations and anions: these can be used as starting point to assign bead types to charged groups in small molecules.
Please post some examples of the parameterization of the small molecules containing charged centers e.g., nitrogen containing heterocycles at physiological pH. or guidelines to treat such centers.