Hannah Baumann

Thank you so much @ijpulidos , this is super helpful! It looks like it's the 5 systems that involve net charge changes. I'll be looking into this!

@ijpulidos : Here are the input `.graphml` files for systems MCL1, TYK2, p38, cdk2, hif2a: [ligand_network_mcl1.graphml.zip](https://github.com/openforcefield/protein-ligand-benchmark/files/15092890/ligand_network_mcl1.graphml.zip) [ligand_network_tyk2.graphml.zip](https://github.com/openforcefield/protein-ligand-benchmark/files/15092901/ligand_network_tyk2.graphml.zip) [ligand_network_p38.graphml.zip](https://github.com/openforcefield/protein-ligand-benchmark/files/15092998/ligand_network_p38.graphml.zip) [ligand_network_cdk2.graphml.zip](https://github.com/openforcefield/protein-ligand-benchmark/files/15093032/ligand_network_cdk2.graphml.zip) [ligand_network_hif2a.graphml.zip](https://github.com/openforcefield/protein-ligand-benchmark/files/15093040/ligand_network_hif2a.graphml.zip)

@ijpulidos : Thank you for looking into this! Since we needed to make a (short term) decision for openfe, I worked on some of the changes mentioned about in this...

@ijpulidos : I had completely forgotten to reply here, sorry about that! I'm still happy to open up a PR regarding the changes here. Do you think that still makes...