ADL: add H

Tomek Wlodarski tomek.wlodarski at
Thu Feb 14 07:57:15 PST 2008

Hi Floren,

Try any molecular modelling software such as: Chimera, Pymol, VMD and
probably many other.
There should be an option to add Hydrogen - depending on software you would
be able to add to selected atom or program would search for any missing
hydrogen atoms.
I hope this would help you.

Tomek Wlodarski

On Thu, Feb 14, 2008 at 12:52 PM, Florenci V. Gonzalez <fgonzale at>

> Hello,
>        during the editing of the PDB file of my molecule I need to delete
> an inhibitor structure attached to it because the inhibitor is
> covalently bound through a C-S bond, then once the inhibitor is
> removed I want to add a hydrogen atom to the sulfur atom of the
> protein and here comes the question: how can I add that hydrogen to
> the sulfur atom before running the docking?
> Thanks.
> Floren
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