[Chimera-users] "Extra" hydrogens in Dockprep and addH steps
adolphsdchiu at ufl.edu
Mon Jan 12 11:54:40 PST 2009
Dear colleagues and friends,
I notice that during "Tools -> Dockprep" and "Tools -> addH" steps
Chimera sometimes will automatically add hydrogens to the
positions considered necessary by the program itself. However,
these positions do not always really have these hydrogens imposed
One situation is when I added hydrogen to the molecule containing
nitrogen with lone-pair electrons, Chimera added hydrogen to the
position of this lone-pair.
One other situation is in the disulfide bond. It seems that
Chimera can not recognize the disulfide bond, so hydrogen is added
to each of the thiol group, which is obviously inappropriate.
I'm wondering what causes these situations and how users can
prevent them happening. Any help is appreciated. If you
coincidently encountered with similar situation, I'm glad to hear
your story as well~
Happy new year and best wishes to your research!
More information about the Chimera-users