AutoDock tool

Fig. 4.38 The menu bar and read molecule option in AutoDock tools (ADT)...

We have to open the command prompt, from the start menu go to all programs, then to command prompt. Before miming Vina in the command prompt, we have to create configuration file in a text doeument which includes the receptor name, ligand name, dimensions, and coordinates of the grid (active site) which we gave in the AutoDock tools (mentioned above). This is named as conf.txt file (Fig. 4.47). 

It gives the protein-binding affinity in kilocalorie per mole (kcal/mol) for every conformation and also the RMSD. automatically detects the processors and displays it. The log files and output files can be seen in the folder. The outfile (out.pdbqt) can be visualized through PyMOL [16] or AutoDock tools (Figs. 4.49 and 4.50). 

Park, H., Lee, J., Lee, S. (2006). Critical assessment of the automated AutoDock as a new docking tool for virtual screening. Proteins Struct. Funct. Bioinf., 65, 549-554. 

These files are converted into. pdbqt format (as they are needed by Autodock Vina) through MGL tools. Click on the autodock icon on your desktop to open the workspace. Go to File menu on the top and then to Read molecule and from there browse the protein. pdb file into the workspace (Fig. 4.38). 

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