ADL: Problems in flexible docking runs AD4

Patrick Pfeffer pfefferp at staff.uni-marburg.de
Thu Jan 10 04:20:13 PST 2008


Hi,

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,
Patrick

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
http://www.agklebe.de
e-mail: pfefferp at staff.uni-marburg.de
*************************************




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