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Docking 1

Docking and Scoring

Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a MLR model for trying to predict the Glide score. Generate the ligand Interaction Diagrams for some poses.

[Requires: LigPrep, Glide, Prime]

Docking and Scoring: Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a MLR model for trying to predict the Glide score. Generate the ligand InteractionDiagrams for some poses.[Requires: LigPrep, Glide, Prime] Calculation distribution controled from the Preferences* LigPrep Run on 4 CPUs of the Primary host set in the PreferencesNumber of subjobs- set automatically to the number of CPUseg -HOST myCluster:4 -NJOBS 4* GlideRun on all the CPUs of the Primary host set in the Preferences Number of subjobs- set automatically to the number of CPUs-HOST myCluster:12 -n 12 * Prime MM-GBSARun on 10 CPUs of the secondary host set in the Preferences -HOST myColleagueMachine:10 -NJOBS 10* RRHO entropyRun on the secondary host set in the Preferences -HOST myColleagueMachine:10Inspect the posesInspect the structures in 2Dand the postprocessing resultsRigid receptorLigands only%file%100 ligands to dock%file%P38 MAPK (1bl7)%file%1 form in 3DSD outputHTVS Run Maestro Table Viewer Prime MM-GBSA Row Filter Molecule Writer(from MAE) Smiles Reader Glide Grid Reader LigPrep Glide LigandDocking Docking and Scoring: Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a MLR model for trying to predict the Glide score. Generate the ligand InteractionDiagrams for some poses.[Requires: LigPrep, Glide, Prime] Calculation distribution controled from the Preferences* LigPrep Run on 4 CPUs of the Primary host set in the PreferencesNumber of subjobs- set automatically to the number of CPUseg -HOST myCluster:4 -NJOBS 4* GlideRun on all the CPUs of the Primary host set in the Preferences Number of subjobs- set automatically to the number of CPUs-HOST myCluster:12 -n 12 * Prime MM-GBSARun on 10 CPUs of the secondary host set in the Preferences -HOST myColleagueMachine:10 -NJOBS 10* RRHO entropyRun on the secondary host set in the Preferences -HOST myColleagueMachine:10Inspect the posesInspect the structures in 2Dand the postprocessing resultsRigid receptorLigands only%file%100 ligands to dock%file%P38 MAPK (1bl7)%file%1 form in 3DSD outputHTVS Run Maestro Table Viewer Prime MM-GBSA Row Filter Molecule Writer(from MAE) Smiles Reader Glide Grid Reader LigPrep Glide LigandDocking

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On NodePit since: 2020-08-12
Last update: 2024-12-17
Created with KNIME version: v4.1.0
Tags: DockingLigPrepGlidePrime

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