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(methods, ff, poses, charges, ….)","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Stages","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"above data","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"+ structures (PDB + poses)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"+ partial charges, FF parameters","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"method, method parameters","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Ligands:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Structure as sdf 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.pdb)","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"generated with gromacs ","type":"text"},{"text":"gmx pdb2gmx","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":" : ‘water+other’, ‘water+cofactors’, ‘other’?","type":"text"}]}]}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Hybrid:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"hybrid struct based on ligand A","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"hybrid struct based on ligand B","type":"text"}]}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Problems with current version:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"partial 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lig_.itp","type":"text"},{"type":"hardBreak"},{"text":"│ │ ├── lig_.top","type":"text"},{"type":"hardBreak"},{"text":"│ │ └── posre_lig_.itp","type":"text"},{"type":"hardBreak"},{"text":"│ ├── lig_","type":"text"},{"type":"hardBreak"},{"text":"│ …..","type":"text"},{"type":"hardBreak"},{"text":"│ └── 03_hybrid","type":"text"},{"type":"hardBreak"},{"text":"│ ├── edge__","type":"text"},{"type":"hardBreak"},{"text":"│ │ └── water","type":"text"},{"type":"hardBreak"},{"text":"│ │ ├── crd","type":"text"},{"type":"hardBreak"},{"text":"│ │ │ ├── mergedA.pdb","type":"text"},{"type":"hardBreak"},{"text":"│ │ │ ├── mergedB.pdb","type":"text"},{"type":"hardBreak"},{"text":"│ │ │ ├── pairs.dat","type":"text"},{"type":"hardBreak"},{"text":"│ │ │ └── score.dat","type":"text"},{"type":"hardBreak"},{"text":"│ │ └── top","type":"text"},{"type":"hardBreak"},{"text":"│ │ └── openff-1.0.0.offxml","type":"text"},{"type":"hardBreak"},{"text":"│ │ ├── ffmerged.itp","type":"text"},{"type":"hardBreak"},{"text":"│ │ ├── ffMOL.itp","type":"text"},{"type":"hardBreak"},{"text":"│ │ └── merged.itp","type":"text"},{"type":"hardBreak"},{"text":"│ ….","type":"text"},{"type":"hardBreak"},{"text":"├── _","type":"text"}]},{"type":"paragraph"}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[430.0]},"content":[{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"parent folder for target ","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"metadata","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"information about edges / perturbations","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"information about 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