ADL: prepare_ligand and python tools

Ruth Huey rhuey at scripps.edu
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 
>John 
>
>________________________________________________
>--- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
>
>  
>
Hi John,

In order  to use the prepare_ligand.py, prepare_dpf.py 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/prepare_ligand.py -l 
yourligand.pdb

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

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 prepare_ligand.py script in REL-1-3alpha2:

--> prepare_ligand.py

AutoDockTools/Utilities/prepare_ligand.py prepare_ligand: ligand 
filename must be specified.
Usage: prepare_ligand.py -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!

             Ruth
  




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