Filter that disallows hybridization changes

OpenFreeEnergy / kartograf

This is an package contains tools for setting up hybrid-topology FE calculations

https://kartograf.readthedocs.io/

MIT License

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Filter that disallows hybridization changes #41

Open hannahbaumann opened 4 months ago

hannahbaumann commented 4 months ago

In some mappings in ligands in the PLB system, mapping atoms that are connected by single or double bonds can lead to problems. It would be great to see if mappings that do not map these hybridization changes would perform better.

Example 1: P38 Edge lig_p38a_2gg - lig_p38a_2ee download

Mapping of sulfone and amide let to "stereo inversion" with OpenMM 8.0.0 Screen Shot 2024-04-10 at 2 15 21 PM

Other example: CDK8 Lig_25 - lig_24

download-1

RiesBen commented 4 months ago

Hi @hannahbaumann , do you think this filter could help you out? https://github.com/OpenFreeEnergy/kartograf/blob/8ef8f8850ed1bbf0afcf656bc80172bd305f5f91/src/kartograf/filters/element_change.py#L54