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Jaguar Minimization

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

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

Icon
Molecules in Maestro format

Output Ports

Icon
Minimized molecules in Maestro format

Best Friends (Incoming)

Workflows

Installation

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

KNIME 4.2
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Developers

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