[Chimera-users] Adding Hydrogens to Dexomethasone Misses 1 Atom

[Elaine Meng]

Dear Batuhan Kav,
It is because the geometry (bond lengths and angles) are different in the two molecules.  Chimera uses these to try to figure out the atom types.  In the "correct" molecule, C6 is identified as atom type C3 (sp3-hybridized carbon), whereas in the "incorrect" molecule, it is identified as atom type C2 (sp2).  

You can manually assign C6 to the correct atom type before adding hydrogens, for example with command:

setattr a idatmType C3 @C6

You can see the atom types by labeling, for example menu "Actions… Label… IDATM Type" to label the currently selected atoms.   You would have to re-label (choose this menu item again) after changing the type to see the change.

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 Aug 26, 2014, at 6:45 AM, BATUHAN KAV <bkav13 at ku.edu.tr> wrote:

> Dear All,
> 
> I am trying to add hydrogen atoms to dexomethasone ligand. In the original PDB file, there are two dexomethasone molecules. So, I create split them into two different PDB's. Then, I load them and use addH option. In one PDB (sil.pdb), everything works fine and all hydrogens are added successfully. However, in the other pdb (which I name as other.pdb), one hydrogen atom is missing. I will use these files for further parametrization in AMBER, so this is really important. I looked through the files over and over again but couldn't find any reason for this apparent difference. What am I missing? I also attach the files. Any help would be greatly appreciated.
> 
> Cheers
> <sil.pdb><sil-2.pdb><other2.pdb><other.pdb>