About OFraMP

OFraMP stands for Online Fragment-based Molecule Parametrisation. This online tool uses fragments of parametrised molecules from the ATB as fragments for a larger target molecule. It identifies potential fragments matches for the target molecule and compares these fragments using a novel hierarchical matching procedure.

An atom within a pre-parameterised model that are selected as part of a fragment for a target molecule is based on whether it and its surrounding atoms match the target molecule. The size of this buffer region is referred to as the shell size. The user can select the shell size.

The user selects matching fragments until the the target molecule is fully parametrised.

If desired, the user can also manually change the charge of individual atoms.

If atom charges cannot be assigned from the available pre-parameterised molecules within the database, the user can send the missing fragment directly to the ATB for processing.

Reference

For a more detailed explanation of OFraMP, please refer to

Stroet, M.; Caron, B.; Engler, M. S.; van der Woning, J.; Kauffmann, A. ; van Dijk, M.; El-Kebir, M.; Visscher, K. M.; Holownia, J.; Macfarlane, C.; Bennion, B. J.; Gelpi-Dominguez, S.; Lightstone, F. C.; van der Storm, T. Geerke, D. P.; Mark, A. E.; Klau, G. W. OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. Journal of Computer-Aided Molecular Design 2023, 37, 357-371.