ConfGen (deprecated)0 ×

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

Update Site

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

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