ADL: Receptor flexible residues

Juan Munoz-Garcia juan.munoz-garcia at
Thu Feb 27 09:57:35 PST 2014

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.

Juan C. Muñoz-García, PhD
Biomembrane Structure Unit
Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU

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