degrootlab / abs_dg_paper_chemscience2021 Goto Github PK

Dear Khalak,

I found there are many clashes when aligning the decoupled structures of ligands in solvent into the apo state pocket. And some of them cannot be solved by just do a minimization and the following calculation cannot continue. Can you please tell me how do you figure out such a problem? For example, in my 165 transition runs, just 60 succeed. I ran a example for cdk2 with ligand 30, but I got a very large dG result (-69.09 kJ/mol) compared to experiment (-42.3 kJ/mol).