ADL: Nested Branches Error

Michel Sanner sanner at
Mon Oct 5 14:32:36 PDT 2020

Hello Linnea

Your PDBQT does not look like an AutoDock ligand, but like a receptor, i.e. the torsion tree describing which bonds in the ligand are rotatable is not defined. How did you generate this PDBQT file ?


From: <autodock-bounces at> on behalf of Linnea Dolph <lsdolph at>
Reply-To: "autodock at" <autodock at>
Date: Monday, October 5, 2020 at 2:29 PM
To: "autodock at" <autodock at>
Subject: ADL: Fwd: Nested Branches Error

I am a new user with autodock and I have gotten this error message:  All
ATOM and HETATM records must be given before any nested BRANCHes; see line
2 in PDBQT file "3oxododecamide.pdbqt".
And I am not sure what I am doing wrong or what I should do to go about
fixing this. Any and all help is greatly appreciated! I have attached the
pdbqt file I am using.
Thank you,
Linnea Dolph

Linnea Dolph
PhD Candidate Franz Group
Department of Chemistry
University of California, Davis

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