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ConfGen (deprecated)

Schrödinger Nodes for Suite2018-1 version 0.0.1.7B27VcMf4_L7A58S5A8G55JS by Schrödinger

The ConfGen node provides access to the Ligand Torsion Search utility, which was developed for rapid and effective systematic ligand conformation generation in Glide. 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
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.
Force field
Available force fields: MMFF, MMFFs, OPLS_2005 (default)
Solvent
valid solvents are: None, Water, CHCl3, Octanol default=None
Electrostatic treatment
electrostatic treatment; possible values are Constant dielectric, Distance-dependent, Force field defined
Dielectric constant
Charges from
Use charges from structure input or Force field
Cutoff
non-bonded cutoffs. valid values are: Normal, Extended, None, User-defined
Van der Waals
Extended non-bonded cutoffs Van der Waals
Electrostatic
Extended non-bonded cutoffs Coulomb
Suppress hydrogen bonding electrostatics
Method
valid minimization algorithms are: PRCG, TNCG, OSVM, SD, FMNR, LBFGS, LTNCG, Optimal
Pre-minimization of input structures
Pre-minimize input molecules using at most this number of iterations (default = 100)
Post-minimization of generated structures
Minimize generated conformations using at most this number of iterations (default = 50)
Converge on
Minimization convergence criterion type (CONV): allowed values: Gradient (default), Energy, Movement, Nothing
Convergence threshold
Minimization convergence criterion (CONV) - default: 0.05
Max number of search moves
ConfGen maximum number of search moves/steps
Use n steps per rotatable bond
Number of steps for AUTO search (AUOP[5]); (i.e., steps per rotatable bond)
Save at most: n conformations per ligand
Maximum number of conformers to retain as the final result for each search performed.
Distinguish mirror-image conformations
Distinguish enantiomers (i.e. do not consider enantiomers to be duplicates)
Search mode
  • rapid = only generate conformers in which at most one peripheral group is rotated away from its lowest internal energy conformation (default)
  • thorough = sample all combinations of rotations of peripheral groups
Amide bonds
  • Vary amide bond conformation (default)
  • Retain original amide bond conformation
  • Set amide bond conformation to trans
Sample rings
ConfGen sample rings
Maximum ring conformations
Confgen maximum number of ring conformations: default=16
Energy window for saving conformations (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 = 25.0).
Compare conformers by
  • None
  • Heavy atoms
  • Heavy atoms plus polar hydrogens (default)
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=0.50).
Maximum torsion angle difference for polar H's (Degrees)
maximum torsional angle difference for polar hydrogens (in degrees)
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: MmodConfGen
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

Installation

To use this node in KNIME, install Schrödinger Nodes for Suite2018-1 from the following update site:

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