[Dock-fans] ligand -regding

John J. Irwin jji at cgl.ucsf.edu
Sat Dec 1 21:46:08 PST 2007

Hi Vinay

It would be helpful for you to tell us a bit more about what program(s)
and options you are using. Which version of docking software? Which
drawing interface?

In general, if you are using a united-atom scoring function, then you
only want polar hydrogens on the protein. If you are using an all atom
scoring function, then you will need all H atoms to be explicit. You
always need (at least for all versions of DOCK) a ligand with all atoms
explicitly represented, for example as found in ZINC.

Good luck


Vinay Kumar wrote:
> Hello dockers,
> I would like to know,
> 1) why is it that only polar hydrogens are added in the macromolecule?
> 2) if we need to add all hydrogens (polar and non-polar) explicitly to
> the ligand while a docking is performed? for ex- if the ligand is
> phenol, do i have to draw the phenyl ring with CH2 explicitly shown,
> or just use the ring structure provided by the drawing interface?
> would like your thoughts,
> regards,
> Vinay
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