ADL: Receptor flexible residues

Oleg Trott trott at
Thu Feb 27 13:39:14 PST 2014


The output file should contain the ligand and the flexible side chains.


On Thu, Feb 27, 2014 at 9:57 AM, Juan Munoz-Garcia
<juan.munoz-garcia at> wrote:
> Dear Autodock Users,
> I've run docking with vina with the --flex flag to account for a set of flexible receptors residues. The calculation ends without any error and the results are what I expected in terms of the ligand conformation. However, when I open the output pdbqt with either Pymol of AutodockTools, only the ligand is displayed. Since I chose the --flex option I was expecting and output file containing individual protein-ligand structures for each docking result, otherwise I can't see the interactions of the flexible receptor residues with the ligand. So, is this a bug or is it how Vina is configured to work? In case it is the latter, what's then the point of the --flex option?
> Thank you very much.
> Regards
> Juan C. Muñoz-García, PhD
> Biomembrane Structure Unit
> Department of Biochemistry
> University of Oxford
> South Parks Road
> Oxford OX1 3QU
> ________________________________________________
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Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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