AutoDock, AutoGrid and the MGLTools for Debian and Ubuntu Linux
There is a series of applications that are key to many in some special communities. The availability of such in Debian, with accompanying helper applications, may be sufficient reason to make people adopt Debian (or one of its descendents) as their next Operating System. One such application is AutoDock.
When we are speaking about AutoDock, we are speaking about many different things:
The AutoDockSuite: implementing the computation of a change in energy that is experienced when a ligand binds to a receptor. This is manifested in the Debian packages
The AutoDockToolkit: the biological preparation of the receptor and the ligand, which comes in many many Debian packages that offer Python packages. Most known are
autodocktools - packaged separately to prepare a protein structure and the (candidate) ligand for docking
vision - packaged as mgltools-vision to graphically specify workflows for protein docking experiments.
So, Debian has all these packages, currently in Testing. The autobuilders for the non-free section have already agreed to accept the MGLTools' non-free packages. Autodock and -grid are already available for Ubuntu since hardy. The MGLTools might just no make it for intrepid. However, the Debian packages can be used without changes for Ubuntu, please consider to give them a try.
aptitude install autodocktools autodock autogrid
The packaging for Debian is maintained together with many other packages in the DebianMed source code managment system. You are welcome to join in - for autodock itself or related packages that you would like to see in your distribution.
Caveats
These packages are a rather recent event and the tutorials provided by upstream do not reflect this yet. When there is a script mentioned that is not available at first sight, please check out the folder '/usr/share/pyshared/AutoDockTools/Utilities24/'. To help Google to find this wiki page, here the contents of that directory:
$ ls /usr/share/pyshared/AutoDockTools/Utilities24/
- Tests pdbqs_to_pdbqt.py prepare_gpf.py summarize_docking_directory.py write_conformations_from_dlg.py pdbqt_to_pdb.py prepare_gpf4.py summarize_results.py write_largest_cluster_ligand.py
compute_AutoDock41_score.py pdbqt_to_pdbq.py prepare_ligand.py summarize_results4.py write_lowest_energy_ligand.py compute_consensus_maps_from_dlgs.py pdbqt_to_pdbqs.py prepare_ligand4.py summarize_time.py write_random_state_ligand.py compute_rms_between_methods.py prepare_covalent_flexres.py prepare_ligand_dict.py summarize_wcg_docking.py write_rigid_ligand.py dpf3_to_dpf4.py prepare_dpf.py prepare_receptor.py superimpose_based_on_subset.py write_vs_hits.py energy_average_maps.py prepare_dpf4.py prepare_receptor4.py superpose_molecules.py gpf3_to_gpf4.py prepare_dpf41.py repair_ligand4.py write_all_complexes.py gpf4_to_gpf3.py prepare_dpf42.py rotate_molecule.py write_clustering_histogram_postscript.py pdbq_to_pdbqt.py prepare_flexreceptor4.py summarize_docking.py write_component_energies.py
$ ls /usr/share/pyshared/AutoDockTools/Utilities24/Tests/
- 1ebg.pdbq ind.pdb ref_1ebg.gpf ref_autodock_parameter_version42.dpf std_ind.pdbq test_prepareLigand.py 1ebg_lig.pdbq ind.pdbq ref_1ebg41.dpf ref_dpf4.dpf std_ind_inactivate_all_torsions.pdbq test_prepareReceptor.py 1ebg_lig.pdbqt ind.pdbqt ref_1ebg42.dpf ref_formatted.pdbqt std_ind_setroot_to_5.pdbq test_prepare_dpf.py 1ebg_rec.pdbqt ligandfiles ref_GALS.dpf ref_hsg1.pdbqt std_ind_with_amide.pdbq test_prepare_dpf4.py ref41_LS.dpf ref_LS.dpf ref_ind.out.pdbq std_no_polar_hydrogens.pdbqs test_prepare_dpf42.py hsg1.gpf ref41_SA.dpf ref_SA.dpf ref_plain.pdbqt std_with_waters.pdbqs test_prepare_gpf.py hsg1.pdb ref4_LS.dpf ref_ad3_dpf.dpf std_gasteiger.pdbqs test_dpf3_to_dpf4.py test_prepare_gpf4.py hsg1.pdbqs ref4_SA.dpf ref_autodock_parameter_version4.dpf std_hsg1.pdbqs test_pdbq_to_pdbqt.py hsg1_ind.dpf ref_1ebg.dpf ref_autodock_parameter_version41.dpf std_hsg1_gasteiger.pdbqs test_pdbqs_to_pdbqt.py
To do for the next release
- change name of binary from runAdt to adt
Popularity-Contest
For an overview on the acceptance of this package, please refer to the popularity-contest page (http://popcon.debian.org for autodocktools or autodocksuite). An equivalent page (with 3-8 times higher numbers) exists for Ubuntu, but their not so comfortable user interface stimulates the preference of the shell as follows:
wget -O - http://popcon.ubuntu.com/by_vote.gz 2> /dev/null | gunzip | egrep 'autodock|mgltool' wget -O - http://popcon.debian.org/by_vote.gz 2> /dev/null | gunzip | egrep 'autodock|mgltool'
Acknowledgements
It should be noted, that the number of Ubuntu installations is higher (close to double) than those on Debian. My respect. Many thanks go to Charles Plessy for the wget Ubuntu GUI substite. External to Debian there is to thank:
- Andreas Mischinski for his support in proving that the packages work for Ubuntu Feisty onwards.
The upstream developers at Scripps for caring for the functionality of their work on Debian/Ubuntu and for these Linux distributions at large
Helping UpstreamThat said, the developers of AutoDock and the MGLtools need to defend the public money that goes into their development by indicating the distribution and acceptance of their work in the community. The availability of these packages are certainly in the strong interest of their public funding agencies, but please
- install the popularity-contest package, so your installation gets counted
register yourself as a user for autodock (at http://autodock.scripps.edu/downloads/autodock-registration). The MGLTools don't have such a registration.
See also
Nice introduction to Debian/Ubuntu and AutoDock
Installation (upstream's packages)
Docking (compatible with these Debian/Ubuntu packages)