ADL: Problems in flexible docking runs AD4

Yang Ye leafyoung at
Thu Jan 10 08:02:23 PST 2008


There are many previous postings about this issue. You can try the 
latest ADT tools for it. But this problem is not difficult to solve by 
modifying the pdbqt file by hand.

PDBQT file for ligand is organized by different blocks, while each 
blocks are a combination of atoms which are not moving relative to each 
other. ROOT, default to be the largest block, is put first. BRANCH are 
other blocks, jointing atoms are specified after BRANCH.
There shall not be nesting (due to topology algorithms in ADT, the error 
was normally towards this). I have also found that it perhaps alright to 
not make the atom number sequential, so one may just move around the 
lines and make a non-nesting PDBQT.

If you are not confident about modification, please be assured that if 
there is anything wrong, it will result in distorted ligand which can be 
easily spotted.

Yang Ye

Patrick Pfeffer wrote:
> 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
> e-mail: pfefferp at
> *************************************
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