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MacroModel Minimization

Minimize molecules 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

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Include Log in output

Include the Macromodel log in the output data table

Force Field

Available force fields: MM2, MM3, AMBER, OPLS, AMBER94, MMFF, MMFFs, OPLS_2005 (default)

Solvent

Available Solvents: None (i.e. vacuum), Water

Minimization Algorithm

PRCG, TNCG, OSVM, SD, FMNR, LBFGS, LTNCG, Optimal

Electrostatic treatment

Force field defined (default), distance dependent, constant dielectric

Dielectric constant

defaults to 1.0

Minimization steps

Maximum number of minimization steps

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: MmodMini
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

: Input data table containing molecules in Maestro format

Output Ports

: Output data table containing minimized molecules in Maestro format

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Workflows

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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