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Ligand alignment MD refinement 2

Workflow

Ligand alignment MD refinement
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime and the RMSDs are reported to assess the pose stability. The workflow can be used to refine for instance on a docking based alignment to prepare the input of a FEP calculation.
Molecular Dynamics
Ligand alignment MD refinementA Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representativeframes are refined with Prime and the RMSDs are reported to assess the pose stability. The workflow can be used to refine forinstance on a docking based alignment to prepare the input of a FEP calculation. - Workflow split in execution and analysis steps- Simplified using Preferences Primary and Secondary host for CPU andGPUDirectorycontaining the cms filesRMSDmatricesLigand file name Representative frames Aligned to reference In the workingdirectoryAlignedIn the working directoryMove to the working directoryon CPU With ligands of the representative framesLigands Matrix file name RMSDTrajectory basenamesand ligand names parsingon a custom msjon GPUAsynchronousList all readingHighlight the filesto analyzeInput PV file complexes and residue renaminginto UNK Working directoryList Files Table Viewer String Manipulation(Variable) Get representative Alignment Processing Loop End (2 ports) CSV Writer Molecule Writer(from MAE) Desmond TrajectoryManipulation Refine protein-ligandcomplexes Column Filter RMSD Group Loop Start String Manipulation(Variable) Align Binding Sites Table Viewer Table Viewer File name Run Desmond Job Control Trajectory Table Viewer Molecule Reader(to MAE) Working directory Protein-ligand Information Table Viewer Ligand alignment MD refinementA Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representativeframes are refined with Prime and the RMSDs are reported to assess the pose stability. The workflow can be used to refine forinstance on a docking based alignment to prepare the input of a FEP calculation. - Workflow split in execution and analysis steps- Simplified using Preferences Primary and Secondary host for CPU andGPUDirectorycontaining the cms filesRMSDmatricesLigand file name Representative frames Aligned to reference In the workingdirectoryAlignedIn the working directoryMove to the working directoryon CPU With ligands of the representative framesLigands Matrix file name RMSDTrajectory basenamesand ligand names parsingon a custom msjon GPUAsynchronousList all readingHighlight the filesto analyzeInput PV file complexes and residue renaminginto UNK Working directoryList Files Table Viewer String Manipulation(Variable) Get representative Alignment Processing Loop End (2 ports) CSV Writer Molecule Writer(from MAE) Desmond TrajectoryManipulation Refine protein-ligandcomplexes Column Filter RMSD Group Loop Start String Manipulation(Variable) Align Binding Sites Table Viewer Table Viewer File name Run Desmond Job Control Trajectory Table Viewer Molecule Reader(to MAE) Working directory Protein-ligand Information Table Viewer

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Nodes

Ligand alignment MD refinement 2 consists of the following 123 nodes(s):

Plugins

Ligand alignment MD refinement 2 contains nodes provided by the following 6 plugin(s):