On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

Journal of Chemical Physics

Volumn 125, Issue 8, 2006, Pages

  Mobley, David L ^a   Chodera, John D ^a   Dill, Ken A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCHEMICAL FREE ENERGY CALCULATIONS; CONVERGENCE PROBLEMS; DOCKING PACKAGES; ORIENTATIONAL RESTRAINTS;

COMPUTER SIMULATION; CONVERGENCE OF NUMERICAL METHODS; CRYSTAL STRUCTURE; DECOMPOSITION; FREE ENERGY; MOLECULAR STRUCTURE; PROBLEM SOLVING; PROTEINS;

BINDING ENERGY;

CATECHOL; CATECHOL DERIVATIVE; LIGAND; PHENOL; PROTEIN;

ARTICLE; BIOPHYSICS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFORMATION; CRYSTALLIZATION; METHODOLOGY; PHYSICAL CHEMISTRY; STATISTICAL MODEL; THEORETICAL MODEL; THERMODYNAMICS;

BIOPHYSICS; CATECHOLS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; CRYSTALLIZATION; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; PHENOL; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 33748252631     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2221683     Document Type: Article

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60. When we refer to orientations in the rest of this work, we mean distinct metastable or stable regions of protein-ligand conformation space the ligand can occupy. Each of these includes some range of ligand motion in each of its six degrees of freedom relative to the protein but is separated from the other orientations by large kinetic barriers.
61. Work by Shirts and co-workers (Refs. 6, 7, 41, and 50) has used the terms decoupling and annihilation to refer to the way in which nonbonded interactions between the ligand and environment are treated. We retain this usage here, as it provides a straightforward way to distinguish the two methods by which these nonbonded interactions are commonly treated in alchemical simulations. Unfortunately for this notation, earlier work by Gilson et al. (Ref. 9) and Boresch et al. (Ref. 3) introduced the term double decoupling method to refer to alchemical free energy calculations performed with distance and/or orientational restraints, as opposed to the double annihilation method used previously (where no restraints are used). These terms imply nothing about how the ligand's nonbonded interactions with the protein are eliminated. Confusion seems inevitable if both of these terminologies are used. Some work has been described as using the double annihilation method with decoupling (Ref. 6), and the present work could be described as employing the double decoupling method with partial annihilation. This is needlessly confusing. Instead, we find it much clearer to simply state whether or not restraints are used, and what type (e.g., distance restraints or orientational restraints), and to describe the alchemical treatment of nonbonded electrostatic and Lennard-Jones interactions separately using the terms decoupling and annihilation. This work therefore employs orientational restraints on the ligand, with the electrostatics annihilated and Lennard-Jones interactions decoupled.
62. Subsequent testing leads us to recommend a PME order of at least 6 and a Fourier spacing of 1.0 Å or smaller for these calculations, as the parameters used here can affect the electrostatic part of the computed free energies significantly for some ligands (but did not affect the convergence properties of interest here).