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Ligand alignment MD refinement 2

Workflow

- Workflow split in execution and analysis steps- Simplified using Preferences Primary and Secondary host forCPU and GPU Directorycontaining the cms filesRMSDmatricesLigand file name Representative framesAligned to reference In the workingdirectoryAlignedIn the working directoryMove to the working directoryon CPU With ligands of the representative framesLigandsMatrix 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 - Workflow split in execution and analysis steps- Simplified using Preferences Primary and Secondary host forCPU and GPU Directorycontaining the cms filesRMSDmatricesLigand file nameRepresentative framesAligned to reference In the workingdirectoryAlignedIn the working directoryMove to the working directoryon CPU With ligands of the representative framesLigandsMatrix 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):