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Chemistry external tool 1-2

Chemistry External Tool Node Use-cases

The Chemistry external tool nodes can be used to parse a log file with basic shell commands, run Shrodinger utilities or backends with specific options. Quick form nodes can be used to create a configuration panel for this node.

[Requires: Maestro, Phase, MacroModel]

- 1rst branch: Run a simple Schrodinger utility
- 2nd branch: Run shell commands
- 3rd branch: Run a Schrodinger product through the command line
- 4th branch: Run a Schrodinger product and control some parameters with a metanode configuration panel
- 5th branch: Run a Schrodinger product and change the parameters by editing the command file

See also:
- Semiempirical NDDO: pass parameter flow variables to the Chemistry external tool node.
- Molecular mechanics - comparison

Chemistry External Tool Node Use-cases: The Chemistry external tool nodes can be used to parse a log file with basic shell commands, run Shrodinger utilities or backends with specific options. Quick form nodes can be used to create a configuration panelfor this node.[Requires: Maestro, Phase, MacroModel]- 1rst branch: Run a simple Schrodinger utility- 2nd branch: Run shell commands- 3rd branch: Run a Schrodinger product through the command line- 4th branch: Run a Schrodinger product and control some parameters with a metanode configuration panel- 5th branch: Run a Schrodinger product and change the parameters by editing the command fileSee also:- Semiempirical NDDO: pass parameter flow variables to the Chemistry external tool node.- Molecular mechanics - comparisonQuery structureShape similarityHitsShape screening2D conversionYou could use the Generate 2D coordinates option of the Molecule to MAE node %file%Options[configurable]ConfGenrun after creatingthe full .com file.ConfGen standardMacroModel .com fileparameter section(can be edited)Inspect theconformationsInspect theconformationsLog20 LigPrepped structures to screen %file%Molecule Reader(to MAE) Extract Properties Table Viewer MAE-to-Smiles ChemistryExternal Tool ChemistryExternal Tool Molecule Writer(from MAE) ChemistryExternal Tool ChemistryExternal Tool Table Creator Run Maestro Run Maestro Table Viewer Molecule Reader(to MAE) SDF Writer Chemistry External Tool Node Use-cases: The Chemistry external tool nodes can be used to parse a log file with basic shell commands, run Shrodinger utilities or backends with specific options. Quick form nodes can be used to create a configuration panelfor this node.[Requires: Maestro, Phase, MacroModel]- 1rst branch: Run a simple Schrodinger utility- 2nd branch: Run shell commands- 3rd branch: Run a Schrodinger product through the command line- 4th branch: Run a Schrodinger product and control some parameters with a metanode configuration panel- 5th branch: Run a Schrodinger product and change the parameters by editing the command fileSee also:- Semiempirical NDDO: pass parameter flow variables to the Chemistry external tool node.- Molecular mechanics - comparisonQuery structureShape similarityHitsShape screening2D conversionYou could use the Generate 2D coordinates option of the Molecule to MAE node %file%Options[configurable]ConfGenrun after creatingthe full .com file.ConfGen standardMacroModel .com fileparameter section(can be edited)Inspect theconformationsInspect theconformationsLog20 LigPrepped structures to screen %file%Molecule Reader(to MAE) Extract Properties Table Viewer MAE-to-Smiles ChemistryExternal Tool ChemistryExternal Tool Molecule Writer(from MAE) ChemistryExternal Tool ChemistryExternal Tool Table Creator Run Maestro Run Maestro Table Viewer Molecule Reader(to MAE) SDF Writer

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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: 2026-01-10
Created with KNIME version: v4.1.0
Tags: ScriptingMaestroPhaseMacroModel

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