ADL: Grid "shifts" during autodock job

Antonio Cavazzuti acavazzuti at
Thu Feb 28 03:08:09 PST 2008

I am working with ADT1.5 , autogrid4 and autodock4 on ubuntu7.1.
I am following docking procedure described in "Using AutoDock 4 with
AutoDockTools:A Tutorial" pdf document. 
I am not able to understand if my problems are due to my faults or something
else.. I am new in Linux environment.
1 - when opening "rigid.pdbqt" for grid construction, after answer YES when  
  asked  if preserve charges, appear a warning window telling me that 

    "NON INTEGRAL CHARGE ON rigid.pdbqt: -1.234
     9 residues are correct

2 - during GRID preparation, I manually (or by "center on ligand" function)  
  set the center of grid around the binding site. In grid parameter file  
obtained the center coordinates are right. After autodock4 job the grid is
placed in another side (far from binding site), and outputted conformations
are localized there (far from binding site). 

Opening .glg file i find a line reporting
  GPF> gridcenter 56.55 -6.064 5.503        # xyz-coordinates or auto

which is the center of grid where I want to perform the docking.   
This line is followed by a section telling that 

  "Grid maps will be centered on user-defined coordinates:

	   	(-0.000, -0.000, -1.238)

   Grid maps will cover the following volume:

                      _______(13.1, 13.1, 13.0)
                     /|     /|
                    / |    / |
                   /______/  |
                   |  |___|__| Midpoint = (-0.0, -0.0, -1.2)
                   |  /   |  /
                   | /    | /
   (-13.1, -13.1, -15.5)      

   Grid map x-dimension :		26.2 Angstroms
   Grid map y-dimension :		26.2 Angstroms
   Grid map z-dimension :		28.5 Angstroms

   Maximum coordinates :		(13.125, 13.125, 13.012)
   Minimum coordinates :		(-13.125, -13.125, -15.488)"

... this is were autodock4 build conformers!! but is not where I want.. Where
am I faulting? 

3 - Opening from ADT1.5 the autodock4 output file (.dlg) a message appears
suggesting me to use "Analyze->Conformations->Show Conformation" to view, but
I can't find such alternative.. To see conformations I can only use
"Analyze->Conformations->play..." command.

4 - The same message cited in point 3 tell me to "type 'my.docked.warnings' in
python shell to list 1 warning message(s) from dlg". I deeply ignore the
python philosophy... so I open ubuntu terminal, I  write "python" and enter.
prompt turns from $ to >>>. I write 'my.docked.warnings'and nothing occurs.
the error message resulting is

  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
  NameError: name 'my' is not defined

... Sorry for the size of the message.. 
Thank you in advance for suggestions :)

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