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:
  1. rec.pdb: Prepared receptor file
  2. 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:

  1. Remove crystallographic waters
  2. Remove hetero atoms