Can I assign protonation states to the molecules?
Yes, you can. Whenever the input files do not contain any hydrogen atoms, eHiTS will evaluate the protonation state on the fly as described in the answer to question the previous question. If the user provides a specific protonation state in the input files, the automatic protonation state handling mechanism will still be invoked as long as the command line argument “-fixproto” has not been used. However, even when -fixproto is not used, eHiTS will use the coordinates of the hydrogens in the input files as optional locations for protons, and will assess whether those are populated or not. The user may wish to run the docking with the pre-assigned protonation state. In this case the user should add to the command line: -fixproto ligand/receptor/both where the user can choose whether to fix the protonation state for the entire system, or only for the ligand or the receptor.
