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

BATUHAN KAV bkav13 at ku.edu.tr
Tue Aug 26 06:45:52 PDT 2014


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
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