ADL: Licensing question 2.0

Stefano Forli forli at
Thu Aug 28 17:57:07 PDT 2014

Hi Jacob,

while we are aware of this difference (still not sure about the source of it, thought), I 
don't think this is a problem because Vina ignores partial charges (see "Why don't the results change when I change the 
partial charges?").
The difference you found are likely to be ascribed to the stochastic search itself.
Hope this helps,


On 08/28/2014 05:51 PM, Dr. Jacob Durrant wrote:
> Hi all. I recently posted a question about MGLTools licensing and got some
> helpful answers:
> In the previous question, several people suggested using openbabel to
> generate PDBQT files in industry, since it doesn't have commercial
> restrictions like MGLTools does. I've experimented with this a bit, and I'm
> not convinced openbabel is a suitable substitute. There are subtle
> differences between the partial charges assigned with MGLTools vs.
> openbabel. For example, look at the partial charges assigned to
> 17-hydroxyprogesterone:
> 17-Hydroxyprogesterone OpenBabelMGLTools -0.293OA-0.293OA0.156C0.149C 0.046C
> 0.053C-0.06C-0.068C -0.007C-0.016C0.002C0.002C -0.003C-0.004C0.002C0.002C
> 0.007C-0.002C0.01C0.013C 0.015C0.019C0.129C0.125C 0.043C0.047C0.008C0.009C
> 0.008C0.01C0.005C0.007C 0.019C0.022C0.016C0.02C 0.032C0.035C0.08C0.084C
> 0.162C0.158C-0.295OA-0.295OA 0.089C0.094C-0.381OA-0.381OA 0.211HD0.211HD
> To see if these subtle differences would impact screen performance, I
> picked 100 random compounds and 18 known inhibitors of one of my favorite
> drug targets and used Vina to dock the babel- and MGLTools-generated ligand
> files.
> Overall, performance was slightly better with the MGLTools-generated ligand
> files, but there were a few ligands where the differences in the best Vina
> scores were quite substantial (1.7 kcal/mol in one case).
> Does anyone know of a program that can give the exact same charges as
> MGLTools? If not, where can I get information about the cost of using
> MGLTools in an industry setting?
> Thanks for your help,
> Jacob
> ________________________________________________
> --- ADL: AutoDock List  --- ---

  Stefano Forli, PhD

  Staff Scientist
  Molecular Graphics Laboratory
  Dept. of Integrative Structural
   and Computational Biology, MB-112F
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: (858) 784-2055
     fax: (858) 784-2860
     email: forli at

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