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MacroModel Conformational Search

Schrödinger extension for KNIME Workbench version 19.2.12.201907261045 by Schrödinger

The Macromodel conformational search node provides access to the conformational search methods Monte Carlo plus Minimization (MCMM), Low Mode Search (LMOD) and a combination of MCMM and LMOD (Mixed mode). For details on the search algorithms see the Macromodel documentation.

Note that for runs that request more than one conformer per input structure, this node will create Maestro cells that contain more than on structure/CT, i.e. a single Maestro cell in the output table may contain more than one structure. Nodes such as the Entropy Calculator can use these cells directly, other nodes may require the use of the Maestro expander (from the Tools category) to convert multi-CT cells in to single-CT cells.

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 replaces Input - 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 file in the output table
Column containing input
Column in the input data table containing molecules in Maestro format
Force field
Available force fields: MM2, MM3, AMBER, OPLS, AMBER94, MMFF, MMFFs, OPLS_2005 (default)
Solvent
  • None (default)
  • Water
Electrostatics
  • forcefield = use dielectric treatment encoded within force field file. All our force fields are supplied, by default, with constant dielectric electrostatics (default)
  • constant = force constant dielectric electrostatics
  • distance-dependent = use distance-dependent dielectric electrostatics
Dielectric constant
Molecular dielectric constant (default = 1.0).
Charges from
Cutoff
  • Van der Waals
  • Electrostatic
  • H-bond
.sbc File
Mini Method
Maximum iterations
Converge on
Convergence threshold
Method
  • MCMM/LMOD (default)
  • MCMM
  • LMOD
Retain mirror-image conformations
By default, a structure and its mirror image are both considered when comparing with the other structures. If one of the two matches, the structure is eliminated. Selecting this option keeps both the structure and its mirror image. This option is useful when stereochemistry is critical for the biological function of the molecule, for example.
MC Steps
The Number of Monte Carlo steps to be carried out (default = 1000).
Energy Window (kJ/Mol)
The window for permissible energy above the lowest-energy conformation. This setting discards any structure that is more than x kJ/mol above the minimum energy conformation (default = 100.0).
Distance cutoff for redundant conformers
The geometric criterion which defines two structures to be identical within a conformational search or a multiple minimization. The search algorithm uses as its criterion not the root-mean-square interatomic distance after optimal rigid-body superposition of a pair of structures, but rather the maximum distance between corresponding atoms after superposition (default=0.25).
Max # of conformers
Maximum number of conformers to retain as the final result for each search performed. All translates to 0 (default), otherwise Max # uses the value in the field.
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: MmodConfSearch
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

Molecules in Maestro format

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.0
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