ADL: Problems in flexible docking runs AD4

Patrick Pfeffer pfefferp at
Thu Jan 10 04:20:13 PST 2008


i have a problem using flexible docking. The error is: all ATOM and  
HETATM records must be given before any nested BRANCHes. see line XX  
in PDBQT file (ligand_file).
The docking is prepared using python scripts from mgltools1.1.4.
If I dock without adding polar hydrogens to the macromolecule, the  
docking works, but the geometries look strange and the scores are in  
the range (+30000)-(+50000)
Rigid docking works fine.

I really hope, someone can help me.

Kind regards,

Mit freundlichen Grüßen,
Patrick Pfeffer

Dipl. Bioinf. Patrick Pfeffer
Arbeitskreis Prof. Dr. G. Klebe
Institut für Pharmazeutische Chemie
Raum A116a
Fachbereich Pharmazie
Philipps-Universität Marburg
Marbacher Weg 6
35032 Marburg  Germany
Fon: 06421/2825908
e-mail: pfefferp at

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