aniketsh

Thank you for getting back, here is my sd file [mol.zip](https://github.com/openforcefield/openff-toolkit/files/12080239/mol.zip) From older version: import openff.toolkit as ot ot.version '0.11.3' [ atoms ] ;num, type, resnum, resname, atomname, cgnr, q,...

conda create -n openff2 -c conda-forge openff-toolkit conda activate openff2 conda install -c conda-forge openff-forcefields

@j-wags This solution worked, thanks. I now understand that the atomtype representation is the newer version has changed, however I am concerned about having long ligand names and then having...

Thanks, @lohedges. My issue, as you describe in option 1, for a membrane system, water molecules are inserted in the membrane. Is there any way to avoid it?

Thank you for this explaination. I am dealing with a situation wherein the water in the topology file is not continuous, for example: Protein 1 Water 4 Ligand 1 Water...