OpenMM Receptor Preparation

This protocol uses PDBFixer to correct most of the common errors encountered in PDB files and prepares it to be used by OpenMM and other programs.

Input

Note

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

OpenMM Receptor Preparation form

The result of this protocol is a AtomStruct, containing the fixed PDB structure, that can be visualized using Analyze Results.

OpenMM Receptor Preparation output

Test

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

scipion3 tests openmm.tests.test_openmm.TestOpenMMPrepareReceptor