Hi Dewey, Chimera guessed the most likely charge state as and assigned the nitrogen the atom type of N3+, which would result in 4 hydrogens added and net positive charge. There is no way it would know which one you wanted from just a single atom in a PDB file… it does not look at the residue name. Chimera uses these atom types: <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/idatm.html> There are several ways you could get neutral ammonia. (A) One way is to open your single-N-atom PDB file and make sure the atom type is set to N3 instead of N3+ before adding hydrogens. First show the type, e.g. commands: labelopt info idatmType label You can see it is N3+. Now select the atom with Ctrl-click and change the type to N3, e.g. command: setattr a idatmType N3 sel ~label label … the latter to refresh the label because it won’t automatically update. Then add hydrogens and charges before saving as Mol2, e.g.: addh addcharge To show charges as labels you could use: labelopt info charge label (B) Another way would be to build from scratch with the Build Structure tool. In the Start Structure panel you could add a single helium atom, then in the Modify Structure panel change that selected atom to N with 3 bonds, tetrahedral. That automatically adds the hydrogens. Then add charges, etc. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 10, 2015, at 3:47 PM, MPI <mpi566@gmail.com> wrote:
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