ADL: Ligand problems

Elizabeth M. Laurenzana eml17 at
Wed Jun 26 14:17:17 PDT 2013


I recently obtained docking results from Vina. When I viewed them in Pymol, a bond was missing between two carbons. I thought this was a bug with Vina, but they suggested that there was no problem, that Pymol is just not showing the bond because the bond distances changed. Is there a way to include the bond? Also, they suggested that there may have been a problem with the way Autodock tools interpreted the ligand. I have attached the ligand and ligand output pdbqt files from autodock and vina. Please see email exchange below.

Thanks for your help,


> I recently downloaded autodock_vina_1_1_2_win32.msi. I had 'success'

>> running vina with my receptor file mEH_Y113H139 and my ligand file

>> DB89epoxide (both pdbqt files were created from pdb files using

>> Autodock tools). The ligand looks fine in the pdbqt file, but in the

>> output file from vina, the docked molecules have changed (a carbon-carbon single bond appears to be removed).

>> Please advise.

>> Thank you,


>> Elizabeth

On Wed, Jun 26, 2013 at 12:46 PM, Oleg Trott <ot14 at<mailto:ot14 at>> wrote:

> Hi


> I looked at your intput molecule in a text editor. It consists of two

> rigid parts: one containing 3 atoms, and another containing 22 atoms.

> These are connected by a rotatable bond.


> The reason you see an extra bond in only one of the two cases is that

> the rotatable bond rotated and some of the distances changed. If you

> are viewing the files in Pymol, it simply tries to guess whether there

> is a bond based on the interatomic distances, so the visualization is

> misleading -- it's not a bug in Vina.


> If you have any further AutoDock Vina-related questions, please

> consider asking them on the AutoDock mailing list and/or in the forum:



> Best,

> --

> Oleg Trott, Ph.D. (Columbia University)


> Staff Scientist in the Olson Lab

> The Scripps Research Institute



By the way, the 3-atom rigid fragment contains two carbons that are marked "aromatic". My guess is that MGLTools was wrong here. You may want to report it here: or in the mailing list (see previous email).


Elizabeth M. Laurenzana, PhD
Center for Molecular Toxicology and Carcinogenesis
Dept of Veterinary and Biomedical Sciences
Pennsylvania State University
304 Life Sciences Building
University Park, PA 16802

814.865.7121 office
501.837.9677 mobile
814.863.1696 fax
Eml17 at<mailto:Eml17 at>

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