[Chimera-users] mol2 for NH3

Dear Users, I try to prepare a mol2 from pdb for ammonia (NH3) and ammonium (NH4+), respectively. I used two commands: addh and addcharge with am1 method. eg, addh addcharge all method am1 It turns out that Chimera gave two similar mol2 files for NH4+ but NOT for NH3. I wonder what command and parameters are needed to produce a correct mol2 for NH3. Here are the input pdb files for NH3 and NH4, respectively. # NH3 HETATM 2860 N NH3 A 402 53.512 -12.964 -36.364 0.88 45.66 N # NH4 HETATM 2858 N NH4 A 404 56.362 -12.467 -27.097 1.00 30.80 N Thanks, Dewey