Application in Free Energy Calculations

In recent literature, many ways have shown how a system can be represented during a free energy calculation. Here is a small taxonomy that tries to capture them and show benefits and disadvantages (more information can be found in [1] [2]):

The hybrid and single topology approaches depend heavily on atom mappings. The mappings are used to find the shared core region of the molecules, such that the atoms part of this region can be represented as one. The single topology approach tries to maximize the number of mapped atoms, where the hybrid topology approach only maps one shared region of the molecules and represents the remaining atom coordinates independent of each other.

The usage of Kartograf’s atom mapper for this application can be found in the turorial: Atom Mapping of two Molecules for finding a common core region.

References

[1]

Ries, B.; Rieder, S.; Rhiner, C.; Hünenberger, P. H.; Riniker, S. - RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. J Comput Aided Mol Des 36, 175–192 (2022). https://doi.org/10.1007/s10822-022-00445-6.

[2]

Ries, B.; Alibay, I.; Swenson, D. W. H; Baumann, H. M.; Henry, M. M.; Eastwood, J. R. B.; Gowers, R. J. - Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations, Chemrxiv (2023) https://10.26434/chemrxiv-2023-0n1pq