H Elanine, Thank you for the detailed suggestions. It works.
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.
I am concerned about the style of "Chimera guessed" because many small molecules and drugs need to be screened. When a small molecule is assigned with partial charges by the command addcharge with am1 method, I noticed that multiple cases failed. With gas method, some cases will pass. However, Chimera gave a warning of unequal to the total formal charge (see below). What do you think about this ? Is it related to idatmType ? If so, it seems to me that one has to exam each atom of a small molecule if the process fails, especially with am1 method. Take NAP as example. eg, a warning of net charge Adding standard charges Charge model: AMBER ff14SB Standard charges added Assigning partial charges to residue NAP (net charge -3) with gas method .... .... (NAP) does not equal to the total formal charge (-4.00) according to the Gasteiger atom type Thanks, Dewey On 6/10/15, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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