[Chimera-users] mol2 for NH3

MPI mpi566 at gmail.com
Wed Jun 10 15:47:00 PDT 2015


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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