ADL: Double bonds in pdbqt file?

Diogo Martins diogo.stmart at gmail.com
Tue Jan 16 15:09:49 PST 2018


Hello,

The .pdbqt file format does not specify bond order, and non-polar hydrogens
are omitted. Therefore, the only difference between C=C and C-C would be a
rotatable bond.

If two carbons are aromatic (either C-C or C=C depending on the resonance
structure), they would be typed "A" instead of "C", and the bond would not
be rotatable.

Pages 27--28 of the AutoDock4.2 user guide describe how rotatable bonds are
defined:
http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide/AutoDock4.2_UserGuide.pdf

Best,


On 16 January 2018 at 13:58, Lubberink, M. <m.lubberink at student.rug.nl>
wrote:

> I am new to molecular docking and am a little bit stuck with the
> preparation of the pdbqt ligand file.
>
> I posted my problem on Researchgate:
>
> https://www.researchgate.net/post/In_ligand_preparation_
> pdbqt_file_for_docking_with_Vina_why_do_C-C_double_bonds_disappear
>
> Hopefully somebody can help me with this,
>
> Thanks in advance,
>
> Max
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