ConfGen Standard

This Node Is Deprecated — This node is kept for backwards-compatibility, but the usage in new workflows is no longer recommended. The documentation below might contain more information.

The ConfGen facility itself uses OPLS_2001 to generate initial trial structures. Minimizations and energy filtering are performed using OPLS_2005 with a distance dependent dielectric constant using a prefactor of 4. This 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 runs will generate more than one conformer per input structure and therefore this node will create Maestro cells that contain more than one 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

$SCHRODINGER/bmin

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

Search strategy
  • Very fast (no energy filtering)—Generate up to 5 conformers per degree of freedom. As conformers are processed eliminate conformers if they have an RMSD value of less than 1.25 Å and all of the dihedral angles involving polar hydrogen atoms are within 60 degrees relative to a previously accepted conformer.
  • Fast—Similar to Very fast except that an RMSD value of 1.0 Å is used to detect redundant conformers, and conformers whose energy is more than 25 kcal/mol (104.67 kJ/mol) higher than the lowest energy conformer are eliminated.
  • Intermediate—Similar to Fast except that 75 conformers are generated per degree of freedom and the quality of ConfGen sampling is enhanced.
  • Comprehensive—Similar to Intermediate except that an RMS value of 0.5 Å is used to detect redundant conformations and the energy window for eliminating candidate structures is increased to roughly 120 kcal/mol (500 kJ/mol).
Minimize input structures
Minimize the input structures before performing the conformational search. This option is not available for the Very fast search strategy.
Minimize the output conformers
This option is not available for the Very fast search strategy.

Input Ports

Icon
Molecules in Maestro format

Output Ports

Icon
Molecules in Maestro format

Popular Predecessors

Popular Successors

Views

Log output of Confgen Standard
Log output of Confgen Standard

Workflows

  • No workflows found

Links

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

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: 23.3.125.v202308020410
On NodePit since: 2023-12-06
Last update: 2023-12-10
Tags: Deprecated
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

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!