Understanding MakeDOCK, which automates sphere and grid generation: Difference between revisions
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=== How to Use MakeDOCK === | === How to Use MakeDOCK === | ||
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# rec.pdb: Prepared receptor file | # rec.pdb: Prepared receptor file | ||
# xtal-lig.mol2 (or .pdb): Ligand specification 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 crystallographic waters | |||
# Remove hetero atoms |
Revision as of 00:15, 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 crystallographic waters
- Remove hetero atoms