Input files (both structure and topology) for the article titled "Caveats and Recommendations for Initial Structure Modeling in Binding Free Energy Calculations".
The content of files in ./Structure_Topology/{PDBID}/ are as follow,
- complex.pdb: coordinates of protein, ligand and crystal waters
- MOL.itp & ffMOL.itp: ligand parameters
- topol_Protein_chain_*.itp/topol.top: protein(s) parameter/gromacs top file
The ddG_data.csv contains the experimental and calculated ddg values using different crystal structures.