I had a query regarding charge assignment to any ligand in chimera. 

While minimizing the energy of a particular ligand (Tools --> Structure Editing --> Minimize Structure) and also during Dock Prep, I found that for most of the aliphatic and alicyclic amines, they are getting protonated with a residual positive charge; while the aromatic amines remain unprotonated (and hence no residual charge). I understand that this is because of their differential pKb values (basic strengths). 

On the other side, deprotonation never occurs with the carboxylic acid (-COOH) group.

Does the Chimera (force fields) control this issue of protonation and deprotonation considering the physiological pH ?

I will be extremely grateful if some one may kindly clarify my doubts.

Thanking you in advance,

With Best Regards,