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Torsion profiles

Torsion_profiles

Performs a torsion scan for a defined dihedral using MacroModel and returns the energy profile.

22.2.4
See more details on https://kni.me/w/QHMlx5jEG_4E8BlC

To define the dihedral, a smarts pattern shared by the submitted structures must be provided, as well as 4 smartsindexes that define the dihedral within the pattern. (Please refer the SMARTS Index Identifier panel in Maestro obtain the index numbers for a smarts pattern)Notes to the energy plot: - The y-axis is set to the maximum of all included structures to allow a direct comparison of energies.Input: - argument 1,SMARTS pattern, e.g., -smarts 'CC(O)c1cc(O)c(O)cc1'- argument 2, SMARTS index, e.g., -index '5,4,2,1'- argument 3, coordinate scan start, stop and step size, e.g., -coordinate_scan_settings '0,360,10'Output:- Torsion energy profile plot- 2D structure with highlighted smarts pattern and dihedral Changelog:22.4.0 - Automatic protocol selection and installation Compound structures from the LiveReportSMARTS%input%SMARTS index%input%coordinate scanparameters %input%Eror messageSMARTs pattern not foundTitle, errorCompound structuresfrom LiveDesign Compound structure input protocolSDF Reader StringConfiguration StringConfiguration StringConfiguration ConstantValue Column Column Filter HighlightSubstructures Get DihedralAtom IDs Preprocessing PlottingPreprocessing MacroModelCoordinate Scan Plot Energy Output Columns LiveDesign Input LiveDesignConnection Upload asLiveDesign Model To define the dihedral, a smarts pattern shared by the submitted structures must be provided, as well as 4 smartsindexes that define the dihedral within the pattern. (Please refer the SMARTS Index Identifier panel in Maestro obtain the index numbers for a smarts pattern)Notes to the energy plot: - The y-axis is set to the maximum of all included structures to allow a direct comparison of energies.Input: - argument 1,SMARTS pattern, e.g., -smarts 'CC(O)c1cc(O)c(O)cc1'- argument 2, SMARTS index, e.g., -index '5,4,2,1'- argument 3, coordinate scan start, stop and step size, e.g., -coordinate_scan_settings '0,360,10'Output:- Torsion energy profile plot- 2D structure with highlighted smarts pattern and dihedral Changelog:22.4.0 - Automatic protocol selection and installation Compound structures from the LiveReportSMARTS%input%SMARTS index%input%coordinate scanparameters %input%Eror messageSMARTs pattern not foundTitle, errorCompound structuresfrom LiveDesign Compound structure input protocolSDF Reader StringConfiguration StringConfiguration StringConfiguration ConstantValue Column Column Filter HighlightSubstructures Get DihedralAtom IDs Preprocessing PlottingPreprocessing MacroModelCoordinate Scan Plot Energy Output Columns LiveDesign Input LiveDesignConnection Upload asLiveDesign Model

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Created by: jcmozzic
Created at: 2021-10-22
On NodePit since: 2022-11-16
Last update: 2026-01-10
Created with KNIME version: v5.2.1
Tags: SchrodingerMacroModelLigPrepLiveDesign

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