[Chimera-users] mol2 for NH3

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 10 16:19:57 PDT 2015

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:

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

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

… the latter to refresh the label because it won’t automatically update.  Then add hydrogens and charges before saving as Mol2, e.g.:


To show charges as labels you could use:

labelopt info charge

(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 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 at 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

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