Receptor preparation

This protocol prepares an AtomStruct object containing a protein file to make it ready for AutoDock tools, such as docking with AutoDock or Vina. Several options for managing non-standard residues, repairing hydrogens and bonds and estimating partial charges are included. It uses the script prepare_receptor4.py in the utilities of AutoDock Tools.

From scipion-chem, we also provide the option of cleaning the structure from HETATM atoms and selecting specific chains from the input structure.

Input

Note

All parameters include a help button that gives further information for each of them.

Receptor preparation form

The result of this protocol is an AtomStruct object containing the resulting pdbqt file of the receptor, ready for other AutoDock tools.

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests autodock.tests.test_autodock.TestADPrepareReceptor