I’m wondering how are aromatic rings treated in PDB files.
If i were to save a small molecule containing aromatic rings or conjugated regions into PDB file, how will GROMACS know which parts of the molecule contain double or single bonds?
Visually, some software may show such molecules as having conjugated bonds, but non-visually, how will they be represented?
Molecular mechanics force fields have no concept of hybridization. Different bond types have different reference lengths and stiffness parameters (force constants). A C-C bond in benzene is shorter and stiffer than a C-C bond in butane, for instance.
Ah I see… Does this mean that as long as conjugation can occur, the atoms involved (mostly carbons and nitrogens) would be described by a specific set of force constants and bond lengths?
That’s correct.
Cool! Thanks Justin