ADL: flexible residues

Frank Neuhaus f-neuhaus at
Thu Jan 8 11:16:47 PST 2009

Hello Dockers,
My question is very simple but alas I don't seem to be able to solve it.  I
am using Autodock4 and am in the midst of testing one, two and no torsions
in a key ARG residue.  Autodock4 works very well with one and two torsions,
but the 'no torsions' is giving me some difficulty.  I need this as a
'control' and would like to use this software version (4)  to examine the no
torsions version, ie.rigid docking 
After preparing the flex file for this docking, I notice that the file is
blank and thus does not work in the docking program.  All coordinates are
gone.  Thus, I gave up on a flex file approach  
To solve this, I followed the procedure recommended by Amit Kessel in
Autodock4 and ADT: short tutorial.  It says: If you are planning rigid
docking, ignore this section (ie preparing the flex residue file) and do the
Grid - Macromolecule - Open [macromolecule PDB file] Save the object as
macromolecule.pdbqt after all charges are added. To continue:
Running autoGrid calculations:
If you are doing rigid docking choose macromolecule.pdbqt file when it asks
Grid - Macromolecule -Open [choose the rigid protein]
In the preparation of the dpf file, choose the macromolecule.pdbqt file for
the rigid file.  Since there is no flex file for the residue, there is
nothing to choose.  The program seems to work, the dlg file lists the
dockings BUT everything both flexible ligand and macromolecule are greatly
distorted and the analysis is unacceptable..  
Somewhere it would appear that I am doing something wrong.  It seems
intuitively simple to correct, but I can't seem to solve it. 
Any ideas out there. 
F.Neuhaus, Northwestern University

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