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Jaguar Minimization

Minimize molecules using Quantum Mechanics

Backend implementation

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

Options

Include log file

Include the Jaguar log file as a column in the output table

Include output

Include the Jaguar output as a column in the output table

Theory

Hartree-Fock, Density Functional (default)

Basis set

lacvp** (default), user-defined

Solvent Model

Only PBF (Poisson-Boltzmann solver) is supported.

Solvent

Select the available solvent from a list: water, cyclohexane, carbon_tet, benzene, chlorobenzenedichloroethane, nitrobenzene, dmso, tetrahydrofuran, chloroform, dichloromethane, dimethylformamide.

Molecular charge

Molecular charge of the input structure(s); note that this setting is applied to all rows in the input table. This option can either be auto: Automatically determine the formal charge of every input structure. or an integer value: set the charge of the molecule explicitly to value

Spin multiplicity

Spin multiplicity of the input structure(s); note that this setting is applied to all rows in the input table

Convergence criteria

Loose convergence criteria performs quicker, coarser geometry optimizations by scaling convergence criteria (iaccg=3)

Maximum Steps

Maximum number of optimization steps/iterations (default=100)

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

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: JaguarMini
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

: Molecules in Maestro format

Output Ports

: Minimized molecules in Maestro format

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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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