ADL: About adding hydrogens for Vina docking

Oleg Trott trott at
Wed Feb 5 11:12:37 PST 2014


The standard ADT protocol for PDBQT preparation is to add all
hydrogens and then "merge" the non-polar ones. Vina was trained and
tested with this protocol, so I suggest following it while using Vina.

On Sat, Feb 1, 2014 at 7:58 AM, Sabri Alpaydın <sabrialp at> wrote:
> Hello. I am using autodock Vina. I get different results when I am docking
> the protein to ligand with all hydrogens or only polar hdyrogens. Which one
> do I have to choose? Which is the best right way for ligand and protein
>  for docking.
> I look forward to hearing from you.
> Thanks in advance for your answers.
> --
> *Assoc. Prof. Dr. Sabri ALPAYDIN*
> Necmetttin Erbakan University
> Ahmet Keleşoğlu Faculty of Education
> Department of Chemical Education
> 42090 Meram/KONYA
> 0332 323 82 20/5494
> 0505 346 68 66
> e-mail: sabrialp at
> <salpaydin at>
> ________________________________________________
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Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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