Vesion 3.0
The files are located in /home/bio/Autodock
The homepage of the program is .
An online manual is available in /home/bio/Autodock/doc/html/documentation.html . (It does not seem to work).
A PostScript version of the manual can be found in  /home/bio/Autodock/doc/manual.p s.
Further instructuions are available in /home/bio/Autodock/doc/ .

On SGI machines:
To run the programs, you have to add two directories to your path:
export PATH=/home/bio/Autodock/bin/sgi4D.IRIX64_6.5_R10000:/home/bio/Autodock/share :$PATH
export AUTODOCK_UTI=/home/bio/Autodock/share

On Linux machines:
To run the programs, you have to add two directories to your path:
export PATH=/home/bio/Autodock/bin/Linux:/home/bio/Autodock/share :$PATH
export AUTODOCK_UTI=/home/bio/Autodock/share
In addition you must ensure that nawk is present, e.g. by putting a link to /bin/gawk (I have put such a link in /home/bio/Bin/Linux).
It is normally also necessary to set (otherwise, you will get segmentation faults or Memory errors)
ulimit -s unlimited

See for some further information how to compile all utility programs at the end of this file.

How to start a calculation

You need the following:
  1. Protein coordinates and charges
  2. Ligand coordinates and charges
  3. A starting structure of the ligand
  4. A box including the expected binding site
How to start the calculation
  1. Start with a pdb structure of the protein (a crystal structure or an equilibrated structure).

  3. Remove alternative configurations (keep the one with the highest occupancy).

  5. Add hydrogen atoms and charges to the structure.
  6. This is done by the first 15 steps in the Amber-equilibration page.
    If you have an equilibrated structure, this is already done, but then you should remove all water molecules instead.
  7. Remove all water molecules.

  8. Remove non-polar hydrogen atoms (adding their charge onto the carbon atom).
  9. This is done automatically by changepdb, command dock .
  10. Run addsol to add atomic solvation parameters.

  11. addsol  protein.pdbq protein.pdbqs
  12. Add hydrogens to the ligand (for example using Spartan) and write a pdb file.

  14. Calculate ESP charges of the ligand at the AM1 level and add to the coordinate file (giving a ligand.pdbq file). Add the charges to the pdb file with the decimal point in column 58.

  15. ATOM      1  A   INH     1       5.475   0.679  -3.852                  0.046
  16. Run atmtobnd to get a connect list for the ligand:

  17. pdbtoatm ligand.pdbq | atmtobnd >ligand.bnd
  18. Define the torsions of the ligand you want to explor during the docking using autotors:

  19. autotors -h -a -A ligand.bnd ligand.pdbq ligand.out.pdbq
    Ensure that you have a picture with atom numbers or names of the ligand when running the program.
    Answer the questions of this interactive program.
    Define any ring system (or any other atom) as root (which is kept rigid).
    Remove non-wanted torsions by writing d followed by a list of the numbers of the torsions you do not want to allow to rotate (one on each line; not that you will not get any further prompt).
    Stop with a c.
  20. Check the ligand charges by

  21. check-qs ligand.out
    (note that you should not give the .pdbq suffix of the  ligand .out.pdbq file). Possible errors are found in the file ligand .out.err.
  22. Construct the grid parameter file (protein.gpf) by

  23. mkgpf3 ligand.out.pdbq protein.pdbq
  24. Construct the docking parameter file (ligand.proteindpf) by

  25. mkdpf3 ligand.out.pdbq protein.pdbq
  26. Edit the protein.gpf file.

  27. You probably want to edit
      npts: the number of points along each coordinate axis (60 60 60 will take about 10 min / conformation)
      spacing: the spacing (in Å) between each grid (ensure that the whole active site fit in)
      gridcentre: the centre of the grid (enter the centre of the active site)
    You should ensure that you have a box that includes the whole protein or the active site. You get the size of the protein and the ligand by changepdb, command size. You can find the size of the active site by running rasmol and select atoms at the end of the active site.
  28. Calculate the potential energy grid maps:

  29. nice -19 autogrid3 -p protein.gpf -l protein.glg&
    This may take a few minutes (e.g. 5 minutes for a 60*60*60 grid).
    Check the result at the end of the file protein.glg:
    Van der Waals energies should range between -10 and 1E+5 kcal/mole, whereas hydrogen bond energies should be -1000 to +1000 kcal/mole.
  30. Edit the ligand.protein.dpf file.

  31. You may want to edit:
      ga_run: the number of final conformations; each conformation takes about one minute.
      #do_local_only: uncomment this line (remove #) and comment out the ga_run line if you only want to minimise the structure
      ga_num_generation: increase these variables if you want longer and more detailed calculations.

  32. Run the docking with
  33. nice -19 autodock3 -p ligand.out.protein.dpf -l ligand.protein.dlg &
    This takes ~10 min for 10 conformations.
  34. The interesting results are found in the ligand.protein .dlg file, especially after the title CLUSTERING HISTOGRAM. There you find the final structures ordered in groups (clusters) of similar structures. The RMSD TABLE give further information, especially the energies.

  35. Next you find the pdb coordinates of the various structures; these can be directly copied into a pdb file to examine the result visually.
    You may also copy all the final coordinates to a file by
    cat protein.pdbq > file; grep ATOM ligand.protein.dlg  | grep -v DOCKED >> file
    You can visualise this file by rasmol and select each docked conformation - they are numbered consecutively from 1 and upwards.
  36. It may be useful to en the simulation by a simple energy minimisation, by uncommenting the line

  37. #do_local_only 50
    in the ligand.protein.dpf file.


Default Lennard-Jones parameters

The parameters are formed according to the normal formulae:
Deafult values:
Atom type
C = A

How to compile some utility programs

some programs are missing in the bin file. They are compled the following way.

cd /home/bio/Autodock/src/autotors
cc autotors.c -o autotors -lm
cd /home/bio/Autodock/bin/sgi4D.IRIX64_6.5_R10000
c ../../src/autotors/autotors autotors

cd /home/bio/Autodock/src/atmtobnd
cc atmtobnd.c -o atmtobnd -lm     (ignore three warnings)
cd /home/bio/Autodock/bin/sgi4D.IRIX64_6.5_R10000
cp ../../src/atmtobnd/atmtobnd .

Follow the instructions in to change the Make file.
In addition we had to make the following two changes:
1. Comment out the following lines in file
    extern "C"
        #include <stdio.h>
        #include "get_atom_type.h"

2. In Makefile, add -static on this row:
autodock3 : main.o $(ADLIB)
        echo $(EXE)'  on  '`date`', using '`hostname` >> LATEST_MAKE
        echo 'Flags: '$(CC) $(LINK) -DNOSQRT -L. -lad $(LIB) >> LATEST_MAKE
        $(CC) $(LINK) -DNOSQRT -static -o $@ main.o -L. -lad $(LIB)

  Follow the instructions in to change the Make file.
In addition comment out the following lines in file get_atom_type.c
    extern "C"
        #include <stdio.h>
        #include "get_atom_type.h"