Authors

Pawel Janowski and Nigel W. Moriarty

Theory and Background

Amber refinement in Phenix combines the power and functionality of Phenix crystallographic refinement

Running refinement with Phenix and Amber

The Phenix user should install the latest AmberTools. Follow the installation instructions and set the AMBERHOME environment variable to point to the Amber installation. This is required for the installation and can be added to the appropriate login script.

To create to bridge between Phenix and Amber, run:

[~:]$ phenix.build_amber_interface

This will create a link to $AMBERHOME in the Phenix installation, reconfigure Phenix to include Amber and build the code required to prepare Amber files and run them seamlessly with Phenix. Amber will remain linked and therefore $AMBERHOME should remain set to the Amber installation.

To run Amber in Phenix, two files need to be created. You can create them using AmberPrep thus:

phenix.AmberPrep 9xyz.pdb

which will generate three files.

4amber_9xyz.prmtop
4amber_9xyz.rst7
4phenix_9xyz.pdb

The first two are the Amber files and the last one is the PDB file that matches the two Amber files for atom order and must be used in phenix.refine replacing 9xyz.pdb. So the refinement command is

phenix.refine 4phenix_9xyz.pdb 9xyz.mtz use_amber=True topology_file_name=4amber_9xyz.prmtop coordinate_file_name=4amber_9xyz.rst7

Here is list of keywords:

REQUIRED KEYWORDS

use_amber - turn on ligand refinement with Amber. (default = False)