Running phenix.refine using Amber gradients (2024)

Principal authors: Nigel W. Moriarty, Pawel Janowski, Hai Nguyen &David A. Case

Contributions from: Jason Swails (Python Sander API), Romain Wolf(pdb4amber which is used in AmberPrep)

Amber refinement in Phenix combines the power and functionality ofPhenix crystallographic refinement with the Amber molecular mechanicsforce field for geometry restraints. Amber restraints replace theconventional set of restraints. In addition to bond, angleand dihedral terms, electrostatics and van der Waalsattractive/dispersive interactions are computed. Calls to Amber'senergy and gradient calculation engines are seamlessly integratedthrough internal libraries shared with Phenix. Refinement with Ambermolecular mechanics has been shown to improve model quality and reduceoverfitting as compared to conventional restraints.

From Phenix 1.16, Amber is distributed with the standard installer forunix and OSX. To run Amber in Phenix, in addition to a PDB file, a topology and acoordinate file must be provided for Amber. From Phenix 1.18,you can allow the phenix.refineGUI to run AmberPrep, automatically creating the files needed. Youcan also easily create these files by using the provided AmberPrep utility viathe AmberPrep GUI or via the commandline:

phenix.fetch_pdb 4Lzt --mtzphenix.AmberPrep 4Lzt.pdb

which will generate four files.

4amber_4Lzt.prmtop4amber_4Lzt.rst74amber_4Lzt.order4phenix_4Lzt.pdb

The first two are the Amber files and the last one is the PDB filethat matches the two Amber files for atom order and must be used inphenix.refine replacing 4Lzt.pdb. Having created the input files, refinement can be run as follows:

phenix.refine 4phenix_4Lzt.pdb 4Lzt.mtz use_amber=True topology_file_name=4amber_4Lzt.prmtop coordinate_file_name=4amber_4Lzt.rst7xray_data.r_free_flags.generate=True

Here is list of keywords:

REQUIRED KEYWORDS

use_amber - turn on refinement with Amber geometry

restraints. ("True" or "False"; default = False)

topology_file_name - relative path to the Amber topology file.

This is the prmtop file created by AmberPrep.

coordinate_file_name - relative path to the Amber coordinate file.

This is the rst7 file created by AmberPrep.

OPTIONAL KEYWORDS

wxc_factor - relative weight factor between the x-ray and

the Amber geometry restraint terms in refinement.By default this is set to 0.1 which multiplies the standard wxc_scalewhich has a default of 0.5 for the x-ray and E&H restraints.(Float; default=0.1)

ADDITIONAL INFORMATION:

1. We also provide the possibility to energetically optimize modelcoordinates using Amber's force field rather than the set ofEngh & Huber restraints. This leads to models of improved quality.This minimization can be run as follows:

phenix.geometry_minimization 4amber_xyz.pdb amber.use=True topology_file_name=4amber_4Lzt.prmtop coordinate_file_name=4amber_4Lzt.rst7

2. AmberPrep contains additional options that the user may wish to use.Run:

phenix.AmberPrep --show-defaults

to view all of the options. Here is a list of the optional keywords:

minimise - type of energy minimization to perform. Possible options:

amber_all - optimize coordinates of all atoms using Amber's minimizer

amber_h - optimize only hydrogen positions using Amber's minimizer (default)

phenix_all - optimize coordinates of all atoms using phenix minimizer

off - do not optimize atoms

clean - remove temporary files (True/False, default=True)

redq - use Amber's redq force field instead of the default (currently

ff14SB). redq is a version of ff14SB that mitigatesthe partial charges on charged amino acid side chains. In theorythis should account for the electrostatic screening effects ofthe unmodelled solvent molecules. In practice our tests have notshown any improvement in refinement when using the reduced charge(redq) force field, but users are free to experiment (True/False,default=False)

3. Refinement with Amber currently has several limitations. All atomsmust be explicitely modelled and there can be no gaps in the peptideor nucleic acid backbone. If hydrogen atoms are missing, they will beadded automatically by AmberPrep but missing heavy atoms should firstbe manually modelled in by the user. Amber does not currently modelalternate conformations and AmberPrep will only retain the firstalternate conformer of each atom. Solutions to these two limitationsare currently in development.

4. Metal-containing ligands are not supported byAmber.

5. Atoms at special positions will most often produce high energyclashes with Amber and usually will not work. If the atom is a solventmolecule, the user may try to refine without it. If the structurecontains atoms at special positions, a warning will be issued whenrunning AmberPrep.

FOR ADVANCED USERS:

1. To use MDGX instead of Sander for gradient calculation, usemd_engine=mdgx keyword for phenix.refine. The default md_engine isSander.

2. phenix.refine with Amber also has a hidden wxc_factor parameter. Inordinary refinement the x-ray term is scaled by the ratio of thegradient norms between the x-ray and geometry terms times thewxc_factor (default 0.5 when using E&H; recommended 0.025 when usingAmber). If wxc_factor is set, the ratio of the gradient norms will beignored and the x-ray term will be scaled by wxc_factor directly. Thisis an experimental feature and has not been shown to improverefinement in any way.

3. The advanced user may wish to change the Amber force field used toimpose geometry restraints. Be default the force field used isff14SB. This can easily be changed by modifing AmberPrep script,run_tleap() method, to source a different force field from Amber.

4. phenix.AmberPrep performs several important actions to preparefiles for refinement with Phenix and Amber. This includes:

1. checks for existence of ligands and non-standard small molecules. Derives Amber parameters using eLBOW and Antechamber
2. cleans and modifies PDB file for conformity with Amber
3. runs TLEaP to prepare Amber topology and coordinate files
4. runs Amber's XtalUtilities to preapre Amber inputs that conform to the given crystallographic space group
5. adds missing hydrogen atoms and possibly missing side chain heavy atoms
6. creates a PDB input file for Phenix that corresponds in atom order and content to the Amber input files