Instructions for running DOCK on Minerva

Running DOCK involves three major steps:

  1. Preparation of the ligand conformational database(s), called flexibase
  2. Running the docking
  3. Extracting results, post processing

1. Preparation of the ligand conformational database

NOTE: This step is not needed if the ligands are from the ZINC database since one can download flexibase versions of their ligand sets.

2. Preparation of the target protein and running the docking

This phase also consists of several steps. The programs and scripts needed are in the directory /sc/hydra/projects/mezeim01b/DOCK_screen.

  1. Define the library paths by typing
    > module load dock
  2. Copy all files from the directory /sc/hydra/projects/mezeim01b/DOCK_screen to your work directory
  3. Make/obtain pdb files for receptor and a ligand at the target site. Save them as rec.pdb and xtal-lig.pdb (keep these names). If the files contain chain IDs, remove them.
  4. Take care of the hydrogens and charges with AutoDockTools (ADT).
  5. Make sure that there is no chain ID (i.e., col 22 is blank) in rec.pdb and xtal-lig.pdb.
  6. Update/create the file hislist with the receptor histidine residues. The file has one line for each histidine residue; each line contains the residue name and the residue number (HIS nnnnnn).
    Make sure that there is no blank line in it. One way to do this is executing
    grep HIS rec.pdb | grep CA | awk '{print $4 " " $5}' > hislist
    where you have to replace HIS with the residue name corresponding to the protonation state used. Also, a space has to be inserted between theresidue name and number in the file hislist. If needed, the Clean operation of Simulaid can remove the chain ID (answer yes when you are asked if you want to override/remove the segmentid).
  7. Cysteines that do not form hydrogen bonds need to have hydrogens (HG) added to them. If they are not present then the following procedure can add them:
  8. Rename H atoms in rec.pdb and xtal-lig.pdb:
    >./ rec.pdb hislist
  9. If there are cysteines forming disulfide bond(s) (i.e., no HSG atoms), change the corresponding residue names from CYS to CYX
  10. Make sure the last record of the pdb file is not TER
  11. Make a copy of the file rec.pdb as rec.crg:
    >cp rec.pdb rec.crg
  12. Execute the Makefile (type make).
    > make
  13. Create folders to run the lead-like database:
    > ./ database_path database_dir 1 1
    where database_path/database_dir is the full path to the directory containing the (gzipped) database file(s)
  14. Submit the docking run by executing the interactive script run_dock.csh

3. Extracting results, post processing

The docking results will be scattered in the directories that the script created. The scripts MUD (Michaels Utilities for Docking) are designed to deal with this situation as follows.

4. How does DOCK work?

Last modified: 06/09/2020