This record is used only when the -z option is active. In practice N iton is always 4 and the four records are for base types A , C , G and T in that order. In the 3DNA model, each base pair, represented by three particles, are connected through CENT to form a long chain. Only CENT has any bulk and advantage is taken of the fact that DNA is locally stiff. This means that the non-bond interactions need to be evaluated for only a small number of atoms.
CENT atoms thereafter.
In practice, k nij is always 4 and the non-bond records are to be given for A , C , G and T in that order. Following the keyword mass is the number of mass records N mass . M i are in units of amu. In practice, N mass is always 12 and four groups of masses are to be given the groups being for the base types A , C , G and T in that order. Each group of masses are for FRON , LEFT and CENT in that order.