[Chimera-users] addH utility and PDB files

Nihshanka Debroy ndebroy at gmail.com
Mon Aug 14 20:38:59 PDT 2006

    I have a couple of questions about the addH utility built into Chimera,
and about PDB files in general. I used addH to protonate (add hydrogens)
to PDB files. Does it use a force field of some kind in the process, like
Amber or Charmm? It seems that depending on the force field used to
protonate a PDB, the values for the partial charges and the van der waals
radii are different. Specifically, I am using these charges and radii in the
    Another thing I've noticed is that when adding hydrogens, for the same
amino acid, the hydrogens are sometimes different in name or number. For
example if I have a Cysteine, in some cases, an HG (gamma hydrogen) is added
for the gamma sulphur, balancing out charges completely. In other cases, the
HG is not added, and so the amino acid ends up with a net negative charge. I
was just wondering if this is supposed to happen.
   Here's another example. For Alanine, I was getting 1H, 2H and 3H attached
to the nitrogen in some cases. In other cases, I just got "H" attached to
the nitrogen. Does this mean those particular instances of ALA in the PDB
had one only hydrogen attached to the nitrogen, instead of 3 ? Wouldn't the
missing 2 hydrogens lead to a net negative charge on the ALA?
   Thanks for all the help and for this mailing list. It is a wonderful

Nihshanka Debroy
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