I want to consider ionization potential for drug molecule before docking using Autodock Vina can any body tell me which tool (free) can be used to do that?
pKa can be modulated by local environment, which may be different for different poses; so the best way is to let the docking algorithm itself assign the most suitable protonation state for each pose. Unreasonable protonation states can be always filtered out after docking (and some unreasonable ones may turn out to be reasonable). With AutoDock, one has to provide the protonation states beforehand.