Understanding MakeDOCK, which automates sphere and grid generation: Difference between revisions
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To prepare a typical pdb structure for receptor use in MakeDOCK, perform the following steps: | To prepare a typical pdb structure for receptor use in MakeDOCK, perform the following steps: | ||
# Remove crystallographic waters | # Remove solvent (i.e. crystallographic waters) | ||
# Remove hetero atoms | # Remove other non-essential hetero-atoms (everything but perhaps a co-factor essential for ligand binding) | ||
# Remove the ligand itself | |||
# Delete all hydrogen atoms | |||
# Save as rec_original.pdb |
Revision as of 00:22, 11 September 2007
How to Use MakeDOCK
- MakeDOCK automates the process of sphere and grid generation for a target.
Input file to MakeDOCK
- The following files are required to specify the target for MakeDOCK:
- rec.pdb: Prepared receptor file
- xtal-lig.mol2 (or .pdb): Ligand specification file
Receptor Preparation
To prepare a typical pdb structure for receptor use in MakeDOCK, perform the following steps:
- 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 hydrogen atoms
- Save as rec_original.pdb