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MD simulation 1-3

Desmond simulation

Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom distance.

[Requires: Desmond] [Keywords: Moleclar dynamics simulation, trajectory, snapshots, jobcontrol, distance, hydrogen bond, atom selection]

Neither the system definition nor the trajectory is saved with the workflow as it can be very large. If you don't want torerun the workflow from the beginning you can still reset and rerun the analysis section (starting from the Alignbinding sites node).This workflow can be run only on Linux. Desmond simulation:Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom distance.[Requires: Desmond] [Keywords: Moleclar dynamics simulation, trajectory, snapshots, jobcontrol, distance, hydrogen bond, atom selection]Initial structure and frames [interactive] atom selectionfor distance measurementeg 2388 - 949 (ligand H bond)HBond numberFirst structureRatioMonitor a specific HBondTotal HBond number in the systemligand-protein HBondsCountAll, no solvent nor counter ionsMonitor the distanceHBond numberBinding siteligand-protein HBondsMonitor a specific HBondHBond numberBinding site onlyHBond number in the systemCreate an archive with the trajectory filesInspect the systemCenter the proteinat the originFrame numberNumber of frames Remove watersInformationon running jobs%file%%file%%file%Very shortsimulationGet PDB Protein PreparationWizard Run Maestro Alignement Desmond SystemBuilder KNIME-MaestroConnector Extract Properties Row Filter Distancemeasurement Math Formula Line Plot (local) Line Plot (local) Table Viewer GroupBy Desmond TrajectoryExtract Frames Line Plot (local) Extract Properties Align Binding Sites Run Maestro Command Run Maestro Command Extract Properties Delete Atoms Run Maestro Command RowID Desmond TrajectoryManipulation Run Maestro ChemistryExternal Tool Math Formula Math Formula Table Viewer ChemistryExternal Tool Job Control CSV Writer CSV Writer CSV Writer Desmond MolecularDynamics Neither the system definition nor the trajectory is saved with the workflow as it can be very large. If you don't want torerun the workflow from the beginning you can still reset and rerun the analysis section (starting from the Alignbinding sites node).This workflow can be run only on Linux. Desmond simulation:Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom distance.[Requires: Desmond] [Keywords: Moleclar dynamics simulation, trajectory, snapshots, jobcontrol, distance, hydrogen bond, atom selection]Initial structure and frames [interactive] atom selectionfor distance measurementeg 2388 - 949 (ligand H bond)HBond numberFirst structureRatioMonitor a specific HBondTotal HBond number in the systemligand-protein HBondsCountAll, no solvent nor counter ionsMonitor the distanceHBond numberBinding siteligand-protein HBondsMonitor a specific HBondHBond numberBinding site onlyHBond number in the systemCreate an archive with the trajectory filesInspect the systemCenter the proteinat the originFrame numberNumber of frames Remove watersInformationon running jobs%file%%file%%file%Very shortsimulationGet PDB Protein PreparationWizard Run Maestro Alignement Desmond SystemBuilder KNIME-MaestroConnector Extract Properties Row Filter Distancemeasurement Math Formula Line Plot (local) Line Plot (local) Table Viewer GroupBy Desmond TrajectoryExtract Frames Line Plot (local) Extract Properties Align Binding Sites Run Maestro Command Run Maestro Command Extract Properties Delete Atoms Run Maestro Command RowID Desmond TrajectoryManipulation Run Maestro ChemistryExternal Tool Math Formula Math Formula Table Viewer ChemistryExternal Tool Job Control CSV Writer CSV Writer CSV Writer Desmond MolecularDynamics

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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On NodePit since: 2020-08-12
Last update: 2024-11-18
Created with KNIME version: v4.1.0
Tags: Molecular DynamcisDesmondTrajectorySnapshotsJobcontrolDistanceHydrogen BondAtom Selection

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