Understanding MakeDOCK, which automates sphere and grid generation

What is MakeDOCK?

• MakeDOCK automates the process of sphere and grid generation for a target.

Makedock Features

• If you have the MakeDOCK Makefile, you simply type 'make' to generate all the spheres and grids.
• All required files and structures will be copied and created for you by MakeDOCK.
• Automatically displays non-fatal WARNINGS that occurred during grid generation, which often lead to incorrect docking results.
• Full dependency resolution means you can change any input or parameter file and type 'make' to generate all files that depend on that change (i.e. tarting or editing spheres).

Input files to MakeDOCK

• Create a new directory containing the following input files to MakeDOCK:

1. rec.pdb: Prepared receptor file
2. xtal-lig.pdb: Ligand specification file

• These are required to specify the target for docking. For help preparing these files, see #Receptor Preparation and #Ligand Preparation below.

How to use MakeDOCK

• In the directory containing rec.pdb and xtal-lig.pdb, do the following to run MakeDOCK.

setenv DOCK_BASE ~mysinger/xyz/dockenv
source ~mysinger/etc/login
cp $DOCK_BASE/scripts/Makefile3 Makefile
make

Making Changes

• Any changes to any file used by MakeDOCK will automatically run all the commands necessary to generate all spheres and grids that depend on that change. For example, tart up a residue in grids/rec+sph.crg and type 'make' to regenerate delphi grids.

MakeDOCK extras

• Once spheres and grids are generated, `make clean` will delete all input and log files, leaving you will the essential output files
• 'make distclean' will remove all files created by MakeDOCK

MakeDOCK as a learning tool

• Look inside the Makefile. The Makefile begins with variable definition and is then divided into target sections. The target sections have been specifically ordered to roughly follow how sphere and grid generation proceeds. Thus the Makefile can be used to learn exactly how spheres and grids are generated for DOCK.

• Variables are set using 'VARNAME = contents'. They are later referenced using $VARNAME. The general syntax for a target section is 'target: dependencies'. Changes to any of the dependencies cause that target to be made. Targets are made using the rules (lines) in that section. The command 'make' actually runs the 'all:' target. You can specify a different target using 'make target'.

Receptor Preparation

To prepare a typical pdb structure for use as the receptor in MakeDOCK, do the following:

1. Remove solvent (i.e. crystallographic waters)
2. Remove other non-essential hetero-atoms (everything but perhaps a co-factor essential for ligand binding)
3. Remove the ligand itself
4. Delete all hydrogens
5. Save as rec_original.pdb
6. Run 'paranoia.csh' to clean up the rec_original.pdb file into a rec.pdb file

Ligand Preparation

To prepare the ligand specification, reload the original pdb structure and perform the following steps:

1. Delete everything BUT the ligand atoms
2. Save as xtal-lig.pdb