ADL: prepare_ligand and python tools

Ruth Huey rhuey at
Thu Feb 10 09:11:28 PST 2005

John Simms wrote:

>Hi All,
>Has anyone used the python tools for preparing the ligand and receptor in the new ADT 1.3. I just cant get them to wor, do i need to access them through ADT ?. Any tips 
>--- ADL: AutoDock List  --- ---
Hi John,

In order  to use the, et al scripts...

1. in the directory which contains the python packages "AutoDockTools", 
"MolKit" etc
        setenv PYTHONPATH `pwd`
<the scripts import various objects from these different packages and 
assume that the python interpreter will be able to find them... which 
requires setting the PYTHONPATH to include that directory>

2. in the directory where you want to use these scripts :
       $PYTHONPATH/AutoDockTools/Utilities/ -l 

  alternatively you could create a symbolic link to the script you want 
to use:
       ln -s  $PYTHONPATH/AutoDockTools/Utilities/ .
  OR just copy the script where you want to use it...
      cp $PYTHONPATH/AutoDockTools/Utilities/ .

fyi: for any of these scripts, you can get a description of the input 
flags it recognizes if you invoke the script with no arguments:

here is a sample from the script in REL-1-3alpha2:


AutoDockTools/Utilities/ prepare_ligand: ligand 
filename must be specified.
Usage: -l filename
    Description of command...
         -l     ligand_filename
    Optional parameters:
        [-v]    verbose output
        [-o pdbq_filename] (output filename)
        [-d]    dictionary to write types list and number of active torsions
        [-A]    type(s) of repairs to make:
                 bonds_hydrogens, bonds, hydrogens, ''
        [-C]    do not add charges
        [-K]    add Kollman charges
        [-U]    cleanup type:
                 nphs_lps, nphs, lps, ''
        [-B]    type(s) of bonds to allow to rotate
        [-R]    index for root
        [-M]    interactive (default is automatic)

     Please let me know if you encounter problems with these new tools!


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