[Chimera-users] mol2 for NH3

MPI mpi566 at gmail.com
Thu Jun 11 11:58:37 PDT 2015


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 at 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 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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