If I have only two options in front of me to select either Gasteiger or the AM1-BCC, so based on which parameters or rules I can select the most appropriate charge scheme during minimization step for my ligand.
Does this has to do anything with my ligand size or the protein size whom I want to dock this ligand?
I have seen some people chose Gasteiger over AM1-BCC, I am confused why preferring an inferior charge algorithm when we have the option for choosing the semi-empirical novel type?
Thanks....