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MacroModel Single Point Energy

Schrödinger extension for KNIME Workbench version 21.1.156.202102141445 by Schrödinger

Calculate the energy of a molecule using MacroModel

Backend implementation

scripts/mmodCLI.py run by cmdRunner.py
The script mmodCLI.py is passed to cmdRunner.py to implement this node.

Options

Include Log in output
Include the Macromodel log in the output data table
High-throughput mode
High-throughput mode runs all structures at once (as opposed to running the script for each row). This is typically faster and is set on by default. If high-throughput mode is OFF and if an input row has grouped CTs, then by default High-throughput mode is still used for that particular row.
Force Field
Available force fields: MM2, MM3, AMBER, OPLS, AMBER94, MMFF, MMFFs, OPLS_2005 (default)
Solvent
Available Solvents: None (i.e. vacuum), CHCl3, Water and Octanol
Electrostatic treatment
Force field defined (default), distance dependent, constant dielectric
Dielectric constant
defaults to 1.0
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: MmodSPE
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option from command line, just specify the option_name and the value as _off_ through the flow variable.

To pick the value from a column in the input table, specify the option_name and the value as :column_name: through the flow variable. Any column other than String, Integer and Double types will be written to a file and the file name is added as the option value.

Input Ports

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Input data table containing molecules in Maestro format

Output Ports

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Output data table containing molecules in Maestro format

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.3

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Developers

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