Autodock for Dummies

Setup

Download autodock_share.zip

Download pmol2q

Remember to append these lines to your .bashrc:

export AUTODOCK_UTI="/home/chuagh/bin/autodock/share"

export PATH=$PATH:/bin/pmol2q_2.3.0_win/src

export PATH=$PATH: /autodock/dist305/bin/linux

Note: You have to change the path according to where you put your share and pmol2q and where your autodoc is installed

Step Through (How to do autodock without using ADT tools

• Example, if you have macro.pdb which contains the marcromolecule and ligand.pdb which is the ligand
• pmol2q macro.pdb macro.pdbqs
• pmol2q ligand.pdb ligand.mol2
• deftors ligand.mol2
• mkgpf3 ligand.pdbq macro.pdbqs [macro.gpf generated]
• mkdpf3 ligand.pdbq macro.pdbqs [ligand.macro.dpf generated]
• autogrid3 –p macro.gpf –l macro.glg
• autodock3 –p ligand.macro.dpf –l ligand.macro.dlg
• get-docked ligand.macro.dlg [ligand.macro.dlg.pdb will be generated. This file contains pdb format of all dockings]

Notes:

• Change rmstol for cluster analysis if you want by editing ligand.macro.dpf

Matlab functions to extract coordinates (download)

• autodock_get_best_cluster_pdb_from_dlg.m
• Usage: autodock_get_best_cluster_pdb_from_dlg(filename)
• Description: extract all docked conformation from the best cluster and put into a single pdb file
• Note that for this function, both .dlg and .dlg.pdb file must be available
• Example: autodock_get_best_cluster_pdb_from_dlg(‘1H24E6’)
• In this example, 1H24E6.dlg and 1H24E6.dlg.pdb must be available
• An output file 1H24E6_best_cluster.pdb will be generated. It contains all pdb coordinates of the docking conformations in the best cluster.
• autodock_get_min_rmsd_from_dlg.m
• Usage: [outline]=autodock_get_min_rmsd_from_dlg(filename)
• Description: Extract the docked conformation which has the lowest rmsd from the starting position
• Note that for this function, both .dlg and .dlg.pdb file must be available
• Example: autodock_get_min_rmsd_from_dlg(‘1H24E6’)
• 1H24E6.dlg and 1H24E6.dlg.pdb must be available
• Output file: 1H24E6_min_ref_rmsd.pdb
• autodock_get_min_energy_from_dlg.m
• Usage: [outline]=autodock_get_min_energy_from_dlg(filename)
• Description: Extract the docked conformation with the lowest docked energy and save as a pdb file
• Example: autodock_get_min_energy_from_dlg('1H24E6')
• Input file: 1H24E6.dlg and 1H24E6.dlg.pdb
• Output file: 1H24E6_min_energy.pdb