Parameters for ADB ligand are obtained from LigParGen web server36–38, LigGerGen provides bond, angle, dihedral, and Lennard-Jones OPLS-AA parameters with 1.14*CM1A or 1.14*CM1A-LBCC partial atomic charges. For charged molecules (ADB linker with net charge -2) CM1A charges are NOT scaled by a factor 1.14.
ADB linker is preoptimized based on the OPLS-AA Force Field, duplicate and move the optimized ligand up by 6 Å, freeze (their X, Y, and Z position will not be updated) skeleton carbon atoms (Supplementary Fig. 11) and optimize the dimer in GROMACS.
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