Understanding MakeDOCK, which automates sphere and grid generation: Difference between revisions
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# rec.pdb: Prepared receptor file | # rec.pdb: Prepared receptor file | ||
# xtal-lig | # xtal-lig.pdb: Ligand specification file | ||
=== Receptor Preparation === | === Receptor Preparation === | ||
To prepare a typical pdb structure for use as the receptor in MakeDOCK, | 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) | ||
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# Remove the ligand itself | # Remove the ligand itself | ||
# Delete all hydrogens | # Delete all hydrogens | ||
# | # Save as rec_original.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 | ||
# Save as xtal-lig.pdb | |||
# Save as xtal-lig. | |||
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:
- rec.pdb: Prepared receptor file
- xtal-lig.pdb: Ligand specification file
Receptor Preparation
To prepare a typical pdb structure for use as the receptor in MakeDOCK, do the following:
- Remove solvent (i.e. crystallographic waters)
- Remove other non-essential hetero-atoms (everything but perhaps a co-factor essential for ligand binding)
- Remove the ligand itself
- Delete all hydrogens
- Save as rec_original.pdb
- 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:
- Delete everything BUT the ligand atoms
- Save as xtal-lig.pdb