Release Notes

v 6.4.4 October 2024

Cube Updates

  • A memory leak bug was fixed in the NESAnalysis cube. The bug could hit the NES floes if a large number of edges needed to be processed.

v 6.4.0 June 2024

General Notice

New Floes

Floe Updates

New Cubes

Cube Updates

  • Fixed a typo in the header of the NES output file nes_output_dataset_result.tar.gz created by the NESResultsToFile Cube. Previously, the header listed DD4G; this has been corrected to DDG. This change should only affect scripted parsing done outside Orion in a manner that relies on the DD4G tag.

  • Fixed a logical error in the NESGMXChimera Cube that previously led NES to ignore user-set number of switches and always run 80 switches when the input datasets came from the :ref: Ligand Bound and Unbound Equilibration for NES <floe_LigandBoundandUnboundEquilibrationforNES[MDPrep][MDRun]> Floe. This issue did not previously emerge when input datasets came from the Short Trajectory MD with Analysis Floe.

  • Added functionalities in NESGMXChimera to detect the presence of protein tumbling restraint information in the Bound Input Dataset and apply them for bound state free energy calculations. This automatically propagates tumbling restraints in NES if they were requested and successfully applied in an upstream Floe that runs equilibrium MD.

v 6.3.6 April 2024

General Notice

Floe Updates

New Cubes

Cube Updates

  • The B-factor Threshold in Percentage parameter has been added to the Docking Checker Cube and the IFP Report Info Gather Cube, to determine the low B-factor binding site residues to evaluate when comparing with the target receptor and computing the fluctuation of the active site during the MD simulation, respectively.

  • The Gromacs Chimeric Cube has been updated to improve the fidelity of alchemical chimeras for polycyclic compounds involving changes affecting which atoms are common to two or more rings. For NES edges affected by this bug fix, users should expect greater computational stability (i.e., fewer switch crashes and no failed edges) and more accurate relative binding free energy predictions.

  • In the NES Floes Equilibration and Nonequilibrium Switching and Nonequilibrium Switching, the Recovery Output Dataset Writer Cube has been replaced by a Record to Record File Converter Cube.

  • In the Nonequilibrium Switching Recovery Floe, the Recovery Dataset Reader Cube has been replaced by a Record File to Record Converter Cube.

v 6.2.1 February 2024

General Notice

  • OpenMM 8.0 and Gromacs 2023.3 support has been added to the Floes.

  • Some major external package dependencies have been updated, including numpy, scipy, and the CUDA toolkit.

  • Bespoke and custom force fields can now be applied to simulation flasks. A bespoke force field is specific to certain ligands or parameters, such as torsion angles, and will override the associated parameters from a general or custom force field. They can be loaded using the Associate Force Field Offxml Files To Ligand Record Floe. A custom force field is a comprehensive force field (presumably with optimized parameters) and will be applied to the entire system when Ligand Force Field in the Force Field Cube is set to Custom and the corresponding custom force field files are uploaded. When providing a custom force field, the general force field will not be used at all.

  • It is now possible to generate smaller simulation flasks by using a rectangular box and applying gentle restraints to the stable portion of a protein to limit protein reorientation. Selection of the stable portion of the protein involved in protein tumbling restraints is automated. This approach can also be used to stabilize a protein for other purposes, such as stabilizing a membrane protein in a water box without including the membrane.

  • v6.2.1 pins orionmdcore==2.3, which includes new features and bug fixes, including a ligand Elf10 partial charge assignment bug fix. Detailed release notes of version 2.3 can be found here: Molecular Dynamics Core Package Release Notes.

  • The Floe Compare Experimental Affinity with Nes Results has been renamed to NES Result Utilities.

New Floes

  • The Associate Force Field Offxml Files With Ligand Record Floe associates bespoke force field files content with the ligand dataset, producing an output dataset that serves as input for subsequent MD Floes calculations. When the bespoke force field content is identified in the dataset, the bespoke force field will be applied to the system if the prefer_bespoke switch in the Force Field Cube is turned On. The prefer_bespoke switch is On by default.

Floe Updates

New Cubes

  • The SMIRNOFF Force Field Files Loader Cube loads SMIRNOFF force field files and associates their contents to the dataset, generating an output dataset.

  • The Specify Protein Tumbling Restraints Cube identifies the stable region of a protein, excluding the binding site, and saves the corresponding restraints information into the dataset.

  • The Bound Protein Ligand MD Health Checker Cube checks if there is restraint information saved on the record when the solvent box is rectangular. If there are no restraints applied to the system and a rectangular box has been selected, the job will be stopped to avoid unwanted interactions between the solute and its periodic images.

Cube Updates

  • Edges involving stereocenter inversion are now less likely to fail during NES runs. Since the introduction of proper stereo handling in version 6.1.2, some users have encountered warning messages of the form “MCS remapping warning: expected N matching atoms after remapping, but got M.” Previously, these warnings may or may not have been associated with an edge failure. In this release, the code has been improved and, though a similar warning may still be emitted, it is expected to be generally benign, and related edge failures should be reduced or eliminated. To assist with issue designation, the relevant message for all such issues is changed to “MCS v2 remapping warning: …” as of version 6.2.1.

  • In the OEMapper Cube Cube, a string parameter, map_type with the options “Default map” and “Star map (with user-selected hub)”, has been added.

v 6.1.7 September 2023

General Notice

  • We have updated some package dependencies:

    • orionmdcore==2.1.2.

    • Openeye-orionplatform==6.0.0.

    • Openeye-snowball==0.26.1.

v 6.1.4 September 2023

General Notice

  • In this release we have mainly focused on minor bug fixing.

Floe Updates

Cube Updates

  • The Gromacs Run Cube has been updated to have better handling of GROMACS warning message control.

v 6.1.2 July 2023

General Notice

  • The Gromacs MD engine to run MD and Free Energy has been updated to the 2022.3 release. This update should have better MD performance in addition to bug fixing.

  • In NES, edges involving stereo center inversion are now supported. Specifically, NES edges involving changes in chirality (both R/S inversion and achiral/chiral site introduction) are now implemented correctly. Prior to this bug fix, directed edges with R->S chiral inversion were implemented as R->R and the reverse S->R transitions were implemented as S->S. This previous behavior led edges connecting two enantiomers to incorrectly estimate relative binding free energies as approximately 0 kcal/mol. Moreover, prior to this bug fix, directed edges representing achiral->chiral conversions may or may not have introduced the intended chirality (though chiral->achiral transitions were correct).

  • Floes for Induced-Fit Posing (IFP), a three-step protocol for the correct prediction of the binding pose of a ligand that requires induced-fit of receptor binding site residue side chains, have been added.

New Floes

Floe Updates

New Cubes

  • MutatedInputChecker This Cube checks if an optional pruned reference receptor is given.

  • ActiveSiteDetectCube This Cube finds an active site from the MDComponents object and saves a list of the active site atom indices.

  • MutateActiveSiteCube This Cube prunes receptor binding site side chains to ALA to allow more space in the binding site, avoiding heavy clashes during docking. The binding site is defined based on the cut-off distance from the cognate ligand of the input reference receptor.

  • SetMapIdxCube This Cube sets the reaction map index property of each atom of the primary molecule to its original atom index.

  • ResetAtomIdxCube This Cube sets the AtomIdx of each atom of the primary molecule to MapIdx.

  • AdditionalPOSITSwitch This Cube switches whether to run an additional POSIT with an additional OEDocking method or not.

  • IFPPositCube This Cube generates relaxed high probability poses for ligands that are analogs of the ligand in the receptor. This cube is suitable for pose generation when working with multiple receptors.

  • POSITGatheringCube This Cube creates one record per ligand for post-processing. The primary molecule of the per-ligand record is the multi-conf mol of the Posit poses.

  • AddReceptorTypeCube This Cube sets the receptor type field to the record.

  • PoseMMPBSACube This Cube computes the MMPBSA score and BintScore from the last frame of the MD stage.

  • MinPoseGatheringCube This Cube creates one record per ligand for post-processing. The primary molecule of the per-ligand record is the multi-conf mol of the minimized poses.

  • ClusterCube This Cube runs clustering for the deduplication of the poses.

  • DockingCheckerCube Given a target receptor to compare, this Cube checks the goodness of the posing results.

  • IFPIDSettingCube This Cube sets the integer ID for each simulation flask as well as a descriptive title string. If the input molecule on a record has multiple conformers, these are split into singles, each with its own ID. If a complex will be formed, this Cube should be used on ligands before forming the complex.

  • IFDMinimizeCube This Cube performs multi-layered restrained energy minimization on the docked pose/reference receptor conformation.

  • ComputeScoreCube This Cube computes the IFP score.

  • ComputeInitScoreCube This Cube computes the step 1 IFP score.

  • IFPBintScoreInitialPoseAndTrajectory This Cube computes the BintScore and iBintScore over the selected frames of the induced-fit trajectory.

  • IFPConcatenateTrajBintScoreCube In this Cube, induced-fit trajectory BintScores and iBintScore are concatenated based on preexisting per-conformer vectors.

  • IFPClusterPopAnalysis This Cube analyzes the induced-fit trajectory clusters in terms of their occurrence, size, and proximity to the starting pose(s).

  • IFDOutputPrepCube This Cube takes the last coordinates from the MDDataRecord and saves the updated DU in the “InducedFitPoseDU” field and updates the primary molecule coordinates.

  • IFPRankSetting This Cube sets the IFP Rank field and resets the primary molecule title with the suffix “_IFP_rankN”.

  • IFPOrderOutputRecords This Cube orders the records of the output dataset based on the IFP Rank field.

  • ExtractClusAvgFromTraj This Cube extracts a main cluster average from the MD trajectory analysis results.

  • PLAnalysisInputCheckerCube This Cube checks if the input dataset is the output dataset of MD Analysis Floes. If True, it emits the input to the failure port.

  • SolvateMDInputCheckerCube This Cube checks if the input dataset is the output dataset of MD Floes. If True, it emits the input to the failure port.

Cube Updates

  • The Gromacs Chimeric Cube has been updated to build a per-frame chimeric molecule. In addition, edges involving stereo center inversions are now correctly handled.

  • The Gromacs Run Cube has been updated to support the 2022.3 Gromacs release.

v 6.0.3 April 2023

General Notice

Floe Updates

  • The MD API Dataset Converter Floe has been updated to support the conversion from datasets serialized by using pickle to new datasets, where the serialization/deserialization is handled by using JSON. The MD Floes have been updated to automatically perform the dataset conversion, and no action is required by the users. However, dataset conversion is required for old datasets produced by custom customer Floes.

  • The Plain Molecular Dynamics Floe, which runs MD simulations in chunks by using a Floe cycle topology to overcome the AWS session limit and make long MD simulations possible in Orion, no longer pins instance type and spot policy. Users can now choose cheaper and faster instances for long MD simulations.

New Cubes

Cube Updates

v 5.6.1 December 2022

General Notice

  • Improved Edge Mapper.

  • Dual-trajectory ensemble MMPBSA support in the Short Trajectory MD with Analysis Floe.

Floe Updates

  • The Edge Mapper for RBFE calculations Floe has two improvements:

    • Alchemical changes between ligands of different formal charges are now allowed. No charge-correction is attempted along the edge at this time; this will change soon.

    • Edge scores are calculated for user provided mapper files.

  • The Short Trajectory MD with Analysis Floe now computes both the single-trajectory and dual-trajectory ensemble MMPBSA scores during the trajectory analysis.

New Cubes

  • 2-traj MMPBSA Cube. This Cube computes the dual-trajectory ensemble MMPBSA.

Cube Updates

  • The OE Mapper Cube has been improved. Now the user provided mapper files are displayed with the calculated edge scores. In addition, edges between ligands with different charges are now allowed although no charge corrections are attempted at this stage during the NES switching. Our testing shows the uncorrected results are still reasonable though we will put in the correction soon.

  • The Affinity Plot Cube has been updated to add the correlation plot of dual-trajectory ensemble MMPBSA vs. experimental data to the existing single-trajectory ensemble MMPBSA and BintScore correlations vs experiment.

v 5.5.3 September 2022

General Notice

In this release we have mainly focused on bug fixing. Improvements have been done of the Chimera MCSS calculation, ligand isomeric SMILES matching, and Chimeric molecule frame alignment.

Cube Updates

  • The RBFECEdgeGathering Cube has been improved for better handling of ligand matching, by using isomeric SMILES.

  • In the NESGMXChimera Cube, the chimera molecule frame alignment, to start the NES switching, has been improved.

Compatibility Notice

  • Mapper Datasets generated prior to the MD Affinity package version 5.0.5 are no longer supported by the NES Floes, and they must be recreated by using the Edge Mapper for RBFE calculations Floe

v 5.5.0 July 2022

General Notice

In this release the major change is the harmonization of the Short Trajectory MD with Analysis (STMD) Floe with Nonequilibrium Switching (NES). Before this, after running STMD, for NES another equilibration run had to be made to get both ligand bound and unbound simulations of adequate length (6ns) for NES. Now this second equilibration run is unnecessary: STMD now runs both both ligand bound and unbound simulations of 6ns by default, producing output datasets ready for input to NES. Plus, you have the trajectory analysis available for those same equilibrium runs. This 6ns default trajectory for STMD is longer and therefore more expensive than the original 2ns run but we think it is an overall savings by not running a whole extra equilibration step for NES. It is easy to simply reset the new default 6ns back to 2ns if you want to have the faster, cheaper STMD run as before.

Additionally:

  • A Freeform analysis of the unbound state has been added to STMD.

  • A new formulation of the BAR overlap metric for the NES work distributions is incorporated into NES edge Floe reports

  • G4/G5 AWS instances are now supported for OpenMM/GROMACS

  • All Floes have a new brief parameter and Floe categories.

New Floes

  • Compare Experimental Affinity with End Point Analysis Results: This Floe is for comparing the short trajectory MD analysis results (binding affinities predicted using the MMPBSA and BintScore methods) with experimental data.

Floe Updates

  • Short Trajectory MD with Analysis (STMD) has been updated to harmonize with Nonequilibrium Switching (NES). STMD now runs both both ligand bound and unbound simulations of 6ns by default. Additionally, freeform is now run on the unbound ligand, producing a separate dedicated dataset.

  • The NES Floes have been updated with a new edge graph Floe report to show the predicted absolute and relative binding affinities. The BAR overlap metric has been added to the NES Floe reports.

  • The Solvate and Run MD Floe is updated to support apo protein simulations.

New Cubes

  • Bound and UnBound Splitting Cube. This Cube emits the primary molecule through the bound port and the standard out port to launch separated ligand-bound/unbound simulations.

  • Unbound FreeForm Cube. This Cube estimates the Gibbs free energy to convert an ensemble of solution conformations into a state where only a single specific conformation is present, and creates XY plot and table image of free energies of conformer ensemble.

  • Unbound Ligand Preparation Cube. This Cube checks whether the primary molecule (ligand) has a single conformer, and reset the title.

  • FreeForm Output Ligand Setting Cube. This Cube reads a Freeform record, chooses starting conformations for unbound MD simulations. The conformations are selected based on the probabilities of state associated with each conformation, and users can choose to ignore the Freeform results and use the bio-active conformation instead.

  • Unbound Traj to OEMol Cube. This Cube converts unbound MD trajectories into a multi-conformer ligand OEMol.

  • Unbound Traj MMPBSA Cube. This Cube computes molecular mechanics potential energies and solvation energies of the unbound MD trajectory snapshots. The Poisson-Boltzmann and Surface Area methods in the OEZap toolkits are used in the solvation energy estimation. The computed energies in the unit of kcal/mol are attached to the record as per-frame vectors of floats.

  • Unbound MD Conformer Gathering Data Cube. This Cube gathers conformer records of a ligand and emits a new single record per ligand. The assembly of the conformer records is attached to the record as a record vector.

  • Unbound Conf Trajs To Ligand Traj Cube. This Cube combines individual conformer trajectory OEMols into single multi-conformer ligand OEMol, in preparation of clustering.

  • Unbound Cluster Ligand Traj OEMol Cube. This Cube clusters unbound ligand multiconf MD trajectory OEMol.

  • Ligand Cluster Selection Cube. This Cube selects frames from the clustering analysis.

  • EdgeFloeReportCube. This Cube generates an edge graph Floe report for the relative and absolute binding affinities.

Cube Updates

  • The OEMapper Cube can also use clustering info to generate the map edges.

  • The NESAnalysis Cube is now calculating the BAR overlap metric for the work distributions.

v 5.0.5 April 2022

New Floes

  • None

Floe Updates

  • The Equilibrium and Nonequilibrium switching Floe now generates a tarball file of key results for download.

  • The Compare Experimental Affinity with NES Results Floe now generates a tarball file of key results for download.

  • The NES Recovery Floe now generates a tarball file of key results for download.

  • The Compare Experimental Affinity with NES Results Floe can now aggregate multiple input datasets to enable users to include the results from previous NES runs.

  • All the Short Trajectory MD Floes are by default pinning g3 spot instances for reliability.

  • All the NES Floes are pinning r5.4xlarge and r5.2xlarge Chimera cube instances for better Gromacs compatibility.

  • MD Analysis Floes are now able to handle any user specified ligand titles, including duplicate ligand titles.

  • In MD Analysis Floes, generating the results tarball file is now optional.

New Cubes

  • DDGAggregator cube. The Aggregator cube aggregates the relative binding affinity results produced by Nonequilibrium Switching runs.

Cube Updates

  • The OE Mapper cube is now sorting the edges by isomeric SMILES.

  • The NES Analysis cube is now setting the output units.

v 5.0.3 December 2021

General Notice

  • Edge Mapper for RBFE calculations

  • Long Trajectory MD supports

  • OpenFF 2.0 support

  • Improved Implicit solvent MD

  • Refactoring

  • Bug Fixing

New Floes

  • Edge Mapper for Relative Binding Free Energies. A starting edge mapper for RBFE calculations mainly based on LOMAP with a new ROCS similarity heuristic

  • Long MD Simulations. Performs long MD simulations starting from the output of the Protein-Ligand or the Solvate and Run MD Floes. The Long MD runs in chunks of max 10 hrs to overcome AWS parallel cube running time limitation

  • MD API Dataset Converter. The old openmm_orion MD pkg have been refactored in multiple pkgs (orionmdcore and oemdaffinity). As consequence a change in the API has happened. The MD API Datatset Converter Floe allows to convert datasets generated from the old openmm_orion pkg version <=4.0.2 to the new API >=5.0.3

Floe Updates

<<<<<<< HEAD * The MD floes and Analysis have now better support for Implicit Solvent Calculations * NonEquilibrium switching floes are now uploading file results ======= * The MD Floes and Analysis have now better support for Implicit Solvent Calculations. * Nonequilibrium switching Floes are now uploading file results. >>>>>>> release_docs_2024_1

New Cubes

  • RBFECMapper cube. The mapper cube produces edges made of ligand pairs to run relative binding affinity calculations starting from a given set of ligands

  • RBFECMapperFloeReport. This cube is designed to work with the mapper cube output to generates the Floe report for the Orion UI displaying the graph of the generated edge map network

  • RBFECMapperResultToFile. This cube uploads a file to Orion with the mapper cube results

  • MDProxyCube cube.The MD Proxy cube runs chucks of MD simulations in cycles till the desired total md running time has been reached

  • MDRecoveryRestartProxyCube. This cube is able to restart or recover a previously run long MD simulation and it is used as support of the MD proxy cube.

Cube Updates

  • All the Protein_Ligand Analysis cubes have been improved to support Implicit Solvent

  • TrajToOEMolCube cube. Performance improvements and long md trajectory support. The frame stride parameter has been added to the list of parameters

v 4.0.1 June 2021

General Notice

  • Nonequilibrium Switching floes for Relative Binding Free Energy (RBFE) affinity calculations

  • New knowledge-based ensemble score BintScore for pose stability

  • Support for taking Posit multi-receptor output as input to protein-ligand MD

  • OpenFF 1.3.1a1 support

  • Bug Fixing

New Floes

  • Nonequilibrium Switching. Relative Binding Free energy calculations and estimate of Binding Affinity, starting from equilibrium MD calculations of the bound and unbound ligands.

  • Ligand Bound and Unbound Equilibration for NES. Performs the equilibrium MD calculations of the bound and unbound ligands needed for NES, starting from an input protein and a set of posed ligands.

  • Equilibrium and Nonequilibrium Switching. Equilibrium MD runs followed by Nonequilibrium Switching, starting from an input protein and a set of posed ligands.

  • Nonequilibrium Switching Recovery. This floe attempts to produce results from uncompleted NES runs, starting from the recovery file.

  • Compare Experimental Affinity with NES Results. Datasets from a completed NES run can be re-analyzed by comparison to a new set of experimental data.

Floe Updates

  • Short Trajectory MD with Analysis. The Bint score analysis has been added and Posit support

  • Analyze Protein-Ligand MD. The Bint score analysis has been added

  • Cofactors have been added to the MMPBSA score calculations

New Cubes

  • BoundUnboundSwitching cube. This cube accept a flask and emit on the bound port the flask containing the a complex while the unbound flask is emitted on the standard output port

  • RBFECEdgeGathering cube. This cube gathers the MD equilibrium simulation data related to the Bound and Unbound simulations and creates edges used to perform relative binding affinity calculations

  • NESGMXChimera cube. This cube generates a chimera molecule and injecting it on select frames from the Bound and Unbound simulations for the Gromacs forward and reverse Nonequilibrium simulations

  • NESGMX cube.This cubes runs the forward and reverse Bound and Unbound starting equilibrium frames by using Gromacs

  • NESAnalysis cube. This cube collects the data generated from the Nonequilibrium runs and calculates the relative binding affinities

  • PlotNESResults cube. This cube generates plots for the Relative binding affinities and the estimated Absolute Affinities versus the provided experimental data. Relevant statistics are calculated and tabled

  • PredictDGFromDDG cube. This cube applies the Maximum likelihood Estimator method to predict the absolute binding affinities starting from the relative binding affinities

  • BintScoreInitialPoseAndTrajectory cube. This cube calculates a trajectory ensemble BintScore relative to an initial pose.

Cube Updates

  • Complex Preparation Cube. This cube has been updated to give better support for clashes detected between the ligands and the other flask components for Posit support

v3.0.1 November 2020

General Notice

  • OpenFF 1.3.0 and 1.2.1 support

  • Bug Fixing

v2.0.0 September 2020

General Notice

  • Ligand centric cluster Analysis

  • New Parametrization Engine

  • OpenFF 1.2.0 (Parsley) support

  • Bug Fixing

New Floes

  • Solvate and Run Protein-Ligand MD. Runs MD on a Protein-Ligand system

  • Analyze Protein-Ligand MD. Performs Energetic and Clustering Analysis on the output produced by the Solvate and Run Protein-Ligand MD Floe

  • Extract Short Trajectory MD results for Download. Extract the results produced by the Short Trajectory MD with Analysis Floe as file to download

Floe Updates

  • A new Equilibration IV stage has been added to the Short Trajectory MD Floe

New Cubes

  • A new MD Components cube has been added to support the new Parametrization Engine

Cube Updates

  • None

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.

  • Generate Ligand Floe Report HTML from Protein-Ligand MD Traj 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 Ligand Traj OEMol 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