ADL: Fw: library docking

Ruth Huey rhuey at
Tue May 2 11:09:39 PDT 2006

Jordi Bujons wrote:

>Hello autodockers,
>I am trying to write a python script that takes a library of ligands (saved, for example, on a single mol2 file) and, having the receptor .map files previously calculated, sequentially initiates Autodock runs for all of them. That means transforming each molecule into pdbq format, defining torsions, assigning charges (or taking those present in the mol2 file), etc... I am trying to use deftors and some of the other utilities included with the Autodock 3.05 distribution. However since I am not an expert programmer, it is taking me quite a bit of time. If somebody from this list has already written such a script, or something similar, and does not mind to share it, I would appreciate it a lot.
>Thanks in advance for your help.
>--- ADL: AutoDock List  --- ---
Hi Jordi,

The most recent release of ADT, available from,  includes a script 
"" designed for processing many ligand files.

It can be used to process many mol2 files in  a foreach loop like this:

foreach f (`ls *.mol2`)
foreach? set name = `basename $f .mol2`
foreach? echo $name
foreach? -l $f -o "$name".pdbqt -d
foreach? end

in this example, a summary of each ligand was written to the optional 
outputfile '' which is specified using -d flag

This is one of several python scripts in AutoDockTools/Utilities, which 
were designed to help format large numbers of input files for autodock.  
These scripts display a usage message when called with no arguments. 

Here is the usage message for which you get by typing 
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
        [-F]    check for and use largest non-bonded fragment (False)
        [-M]    interactive (default is automatic)
        [-I]    string of bonds to inactivate composed of
                   of zero-based atom indices eg 5_13_2_10
                   will inactivate atoms[5]-atoms[13] bond
                               and atoms[2]-atoms[10] bond
                      (default is '')
        [-Z]    inactivate all active torsions
                      (default is leave active)


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