ADL: Ligands and Hydrogens

Bagdevi bagdevi.mishra at
Tue Jun 23 23:59:32 PDT 2009

Use the "" script with following options. -l <ligand_file> -U lps

This will not remove your non polar hydrogens, it will merge charges
and will remove lone pairs, if you want to keep your original charges
and lone pairs as well, you can run the script as follows -l <ligand_file> -U ' '

Bagdevi Mishra.

On Wed, Jun 24, 2009 at 7:40 AM, <kbarakat at> wrote:
> Hi
> Is there a way to keep all hydrogens in the ligand.pdbqt files and not
> to merge non-polar hydrogens. My plan is to use Molecular Dynamics
> simulations to calculate the binding energies of several
> Receptor-Ligand complex starting from the proposed docked structures.
> My major problem in that is: AutoDock merge the hydrogens of the
> ligand and it's very hard to track them back to the initial
> protonation states even with programs like open babel.
> Thanks for your time and your help is so much appreciated
> With my best regards
> Khaled
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