Thereafter, its chemical identicality is ensured by iteratively removing atoms from it until the charge tolerance criteria are met. The simplest approach to do so is to remove the atom with the highest charge difference in each iteration. Alternative approaches are to prioritise the removal of terminal atoms or atoms bordering the alchemical region or both. Our automated TIES topology builder tries all these approaches separately and chooses the one yielding the largest MCS while achieving the charge tolerance criteria. MCS is represented with a unique set of atoms in the simulation-ready system, whereas the remainder of the ligand constitutes the alchemical region. The alchemical regions for ligands corresponding to λ = 0 and 1 states are named "disappearing" and "appearing" regions respectively. In the simulation-ready model, both disappearing and appearing regions are connected to the unique MCS through single bonds. Thus, there is no need to use any position restraints in our simulations unlike the case with the standard dual topology scheme where the entire ligand is coupled/decoupled with the environment. Nor does it require introducing any dummy atoms (that is atoms introduced to account for the imbalance in the number of atoms between the two ligands and which remain fully non-interacting with their neighbouring atoms when the smaller of the two ligands is fully coupled with the environment) unlike their occurrence within the single topology scheme. The modified dual topology scheme used in TIES thus overcomes the drawbacks of both single and dual topology schemes.