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YANK 0.14.1: Early Access 1.0 Release
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@Lnaden Lnaden released this 06 Dec 18:21
· 1470 commits to master since this release
0.14.1
385e530

This release marks the early access phase for YANK 1.0. We intend for this to be a formal release for users to test YANK and its functionality while we refactor the underlying Python API.

In this release:

  • YAML Syntax Structure Frozen. YANK YAML Version 1.0. All YAML scripts from this version will be compatible with future versions until YAML 2.0
    New features may appear in the time meantime, but scripts will be forwards compatible.
  • Initial support for OpenMM XML systems and PDB files
  • Support for separate solvent configurations for the two phases when defined from amber/gromacs/openmm files
  • clearance in YAML no mandatory parameter of explicit solvent, but only when molecule setup goes through pipeline
  • Boresch Orientational Restraints fully implemented and documented.
  • Long range anisotropic dispersion correction improved to work on both ends of thermodynamic cycle leg
  • Documentation updated with better algorithms and theory sections.
  • Full walkthroughs of yank-examples added to online documentation
  • Various other documentation improvements
  • Support for upcoming OpenMM 7.1 Release and features (still works with 7.0.1)
  • YANK now on MIT License
  • Many bugfixes

Validation

YANK has been validated for binding against T4-Lysozyme with the binders: Benzene, Ethylbenzene, Isobutylbenzene, and Indene with the FF14SB Amber Force Field. Our binding free energies match those in the following paper within error:

David L. Mobley, Alan P. Graves, John D. Chodera, Andrea C. McReynolds, Brian K. Shoichet, and Ken A. Dill.
Predicting absolute ligand binding free energies to a simple model site.
J. Mol. Biol. 371:1118, 2007. [DOI]

We have also validated YANK hydration free energies against a reduced set in the FreeSolv Database in TIP3P water based on construction from SMILES strings. The molecular list can be found here. The paper we compared against can be found here:

David L. Mobley and J. Peter Guthrie.
FreeSolv: a database of experimental and calculated hydration free energies, with input files.
J. Comp.-Aided Mol. Design 28:7, 2014 [DOI]

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