ADL: Adding Non-Polar Hydrogens

Amjad Farooq amjad at
Sun Mar 9 16:42:14 PDT 2014

Hi everyone,

I am trying to virtual screen a large library of small molecules
(ligands.mol2) downloaded from ZINC using AutoDock4 on a linux workstation.
Please note that I am running AutoDock on the command line with zero
interface with the GUI.

Everything works fine, however, the PDB files for both the "protein" and
ligands contain polar hydrogens only. How do I add hydrogens to all atoms,
not just the polar ones?

For example, when preparing ligands, I have tried the command below but to
no avail:
> pythonsh -l $f -A hydrogens
where $f refers to each of the ligand .pdbqt files.

After some reading, I understand that the addition of "hydrogens" to all
atoms within a PDB file relies on PyBabel. On my linux machine, the PyBabel
scripts are located at:
However, I am not sure if they are properly installed. How do I ensure that
PyBabel is working? Or any other suggestions as to how to add hydrogens to
all atoms?

Any advice would be greatly appreciated.

Thank you so much.

*AMJAD FAROOQ PhD DIC | Associate Professor*Dept of Biochemistry, University
of Miami School of Medicine
*Location*:  Gautier Building, Suite 217
*Address*:  1011 NW 15th Street #217, Miami , FL 33136, USA
*Contact*:   amjad at | 305-243-2429
*Labpage*: <> |<>

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