Understanding MakeDOCK, which automates sphere and grid generation: Difference between revisions

From DISI
Jump to navigation Jump to search
No edit summary
No edit summary
Line 8: Line 8:


# rec.pdb: Prepared receptor file
# rec.pdb: Prepared receptor file
# xtal-lig.mol2 (or .pdb): Ligand specification file
# xtal-lig.pdb: Ligand specification file


=== Receptor Preparation ===
=== Receptor Preparation ===


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


# Remove solvent (i.e. crystallographic waters)
# Remove solvent (i.e. crystallographic waters)
Line 18: Line 18:
# Remove the ligand itself
# Remove the ligand itself
# Delete all hydrogens
# Delete all hydrogens
# Renumber residues to be monotonically increasing
# Save as rec_original.pdb
# Save as rec.pdb
# Run 'paranoia.csh' to clean up the rec_original.pdb file into a rec.pdb file


=== Ligand Preparation ===
=== Ligand Preparation ===
Line 26: Line 26:


# Delete everything BUT the ligand atoms
# Delete everything BUT the ligand atoms
# Add hydrogens and charges (optional but advised)
# Save as xtal-lig.pdb
# Save as xtal-lig.mol2
 
===

Revision as of 00:46, 11 September 2007

What is MakeDOCK?

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

Input files to MakeDOCK

  • The following files are required to specify the target for MakeDOCK:
  1. rec.pdb: Prepared receptor file
  2. xtal-lig.pdb: Ligand specification file

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
Retrieved from "http://wiki.docking.org/index.php?title=Understanding_MakeDOCK,_which_automates_sphere_and_grid_generation&oldid=4567"