Release Notes

v1.0.0

General Notice

  • Support for OpenFF 1.1.0 (Parsley), the March 2020 release from the Open Force Field Initiative
  • Support for Cuda 10.0
  • Exposed a new parameter in the TrajToOEMol Cube to set the water cutoff distance. This distance is used to select water molecules around the protein-ligand binding site for each trajectory frame and producing a multi conformer water molecule
  • Improved Documentation

New Floes

  • None

Floe Updates

  • New default parameters have been set on the STMDA floe

New Cubes

  • None

Cube Updates

  • None

v0.9.6

General Notice

  • Support for the two force fields from the Open Force Field Initiative: Smirnof99Frosst and OpenFF 1.0.0 (parsley)
  • A new automatic color style is applied to the clustering in the Short trajectory MD analysis to match the cluster colors in the Floe Report
  • Fixed a wrong setting in the Solvation Cube that was placing solvent molecules too close to the solute. This could have produced un-realistic results for some systems where water molecules could have been placed inside proteins
  • Fixed a bug in the GAFF/GAFF2 force field where 1-4 interactions were not correctly scaled
  • Fixed a bug related to un-wanted ligand atom re-ordering
  • Fixed a bug in the protein-ligand active site depiction

New Floes

  • A new Plain Gromacs floe has been added to perform MD by using Gromacs .tpr files

Floe Updates

  • The Yank solvation free energy floe has been removed

New Cubes

  • None

Cube Updates

  • The force field parametrization cube now support open force field 1.0.0 (parsley)
  • The trajectory to multi conformer cube is now adding to the record protein-ligand binding site close waters. These are used to perform MMPBSA calculations with explicit water

v0.9.4

General Notice

  • Upgrades to the trajectory analysis in floe Short Trajectory MD with Analysis expose key results to the Analyze page and 3D visualization page in Orion.
  • Fixed bug in setting restraints in GROMACS cubes.
  • Fixed bug in ordering results in the floe report in floe Short Trajectory MD with Analysis.

New Floes

  • The MD Spruce Prep Floe has been removed. Proteins must be prepared with the Spruce Prep floes available in the Classic
    floes now.
  • The calculation of MMPBSA can now be also performed by using explicit waters (still experimental)

Floe Updates

  • The MD Spruce Prep Floe has been removed
  • The Simple MD Floe has been renamed the Plain MD Floe

New Cubes

  • A new cube has been developed to check the record size before writing to the Orion backend
    to avoiding floe failures. The new cube has been added to all the floes for sanity check.
  • A new cube to estimate the water number around a ligand-protein complex has been developed. The cube is
    used in the MMPBSA calculation with the explicit water flag set on

Cube Updates

  • Exposed MMPBSA ensemble average and standard deviation in the Trajectory Poisson-Boltzmann and Surface Area Energies so that it can be displayed in the Analyze page in Orion.
  • Extract relevant outputs of MD Traj Cluster Analysis now generates trajectory average and median molecules for protein and ligand, with one conformer for each major cluster. These are exposed int the 3D visualization page in Orion.
  • Cluster Protein-Ligand Traj OEMols now exposes a link to the per-ligand floe report page so it is available in the Analyze page in Orion.
  • In Complex Preparation traditional references to the full periodic supermolecular ensemble as a “system” have been replaced with references to a “flask” by analogy with an assay well.
  • In MDFloeReportCube the floe report now generates tiled links to individual ligands in the same order as the initial list of ligands.
  • In MDFloeReportCube the floe report tiles now show how many major clusters were found for each ligand.
  • In NPT Cube and NVT Cube the restraints are now correctly set in GROMACS for proteins consisting of multiple chains.
  • Hint interactions and Styles have been removed from receptors and ligands in the Protein, Ligand and FF parametrization
    setting cubes that could cause problems along the MD analysis stages (debugging is in progress)
  • A bug has been fixed in the ligand Elf10 charging cube that was causing problems when carboxylic acid was present
    in a ligand to be charged
  • The Trajectory to OEMol, Interaction Energies and PBSA calculation cubes have been updated to account for the explicit
    water in the new MMPBSA calculation