2018 DOCK tutorial 1 with PDBID 2NNQ
This tutorial contains, a step by step by approach to dock a known ligand to a known receptor.
The tutorial will be based on the PDB file 2NNQ downloaded from the PDB Database. 2NNQ is the crystal structure for a human adipocyte fatty acid binding protein in complex with ((2'-(5-ethyl-3,4-diphenyl-1H-pyrazol-1-yl)-3-biphenylyl)oxy)acetic acid.
Organization of Directories
Maintaining a clearly organized set of folders will be helpful in finding specific files, calling different files in input files and most importantly keeping track of everything you do. We would like to recommend to maintain the following set of files throughout the tutorial.
0.files 1.dockprep 2.surface_spheres 3.gridbox 4. 5. 6. 7.
II. Preparation of the ligand and receptor
Download the pdb file 2NNQ from PDB database save it in 0.files folder.
Checking the structure
- Read the article related to the PDB file to understand protonation states, charges, environmental conditions and other important information regarding the receptor and the ligand. - Open the pdb file through chimera and look at the structure. Identify the main components of the model (receptor, ligand, solvent, surfactants, metal ions) - Carefully look to identify if there are any missing residues or missing loops. (This particular PDB file didn't contain any missing loops or missing residues)
Preparation of receptor
- Open the PDB file (2NNQ.pdb) via Chimera - Isolate the receptor using select tool and delete tool in Chimera. - Save the isolated receptor as a mol2 file. (2nnq_rec_noH.mol2)
- Open 2nnq_rec_noH.mol2 file again using Chimera and use the following instructions to prepare the receptor file to be used in DOCK. Tools -> Structure Editing -> Add H (To add Hydrogen atoms) Tools -> Structure Editing -> Add Charge (To add the charge use the latest AMBER force filed available for standard residues. Here we used AMBER ff14SB) Save as a mol2 file. (22nq_rec_withH.mol2)
- If you follow the step below all the above stated steps will automatically appear one after the other to prepare the receptor. Tools -> Structure/Binding Analysis -> DockPrep
Preparation of ligand
- Open the PDB file via Chimera. - Using Chimera, isolate the ligand, add H atoms, add charge and save it as a mol2 file by following the same steps followed for the receptor.
Once all the files are prepared make sure to save the files in 1.dockprep folder.