examples for the charged small molecule

[athar91]

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.

[ricalessandri]

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.