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Torsion profiles

Torsion_profiles

Performes 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 supplied, as well as 4 smartsindex that define the dihedral within the supplied pattern. (Please note the SMARTS Index Identifier panel in Maestro to get the index numbers for a smarts pattern)Notes to the energy plot: - The y-axis is adjusted 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:- plot of energies- 2D structure with highlighted smarts patter and dihedral Changelog:22.4.0 - Automatic protocol selection and installation Compound structures from the LiveReportSMARTS%input%SMARTS index%input%coordinate scanparameters %input%Compound structure input protocolLiveDesignEror messageSMARTs pattern not foundTitle, errorCompound structuresfrom LiveDesignSDF Reader StringConfiguration StringConfiguration StringConfiguration Upload asLiveDesign Model CredentialsConfiguration ConstantValue Column Column Filter HighlightSubstructures Get DihedralAtom IDs Preprocessing PlottingPreprocessing MacroModelCoordinate Scan Plot Energy Output Columns LiveDesign Input To define the dihedral, a smarts pattern shared by the submitted structures must be supplied, as well as 4 smartsindex that define the dihedral within the supplied pattern. (Please note the SMARTS Index Identifier panel in Maestro to get the index numbers for a smarts pattern)Notes to the energy plot: - The y-axis is adjusted 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:- plot of energies- 2D structure with highlighted smarts patter and dihedral Changelog:22.4.0 - Automatic protocol selection and installation Compound structures from the LiveReportSMARTS%input%SMARTS index%input%coordinate scanparameters %input%Compound structure input protocolLiveDesignEror messageSMARTs pattern not foundTitle, errorCompound structuresfrom LiveDesignSDF Reader StringConfiguration StringConfiguration StringConfiguration Upload asLiveDesign Model CredentialsConfiguration ConstantValue Column Column Filter HighlightSubstructures Get DihedralAtom IDs Preprocessing PlottingPreprocessing MacroModelCoordinate Scan Plot Energy Output Columns LiveDesign Input

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Created by: jcmozzic
Created at: 2021-10-22
On NodePit since: 2022-11-16
Last update: 2024-04-24
Created with KNIME version: v4.6.1
Tags: SchrodingerMacroModelLigPrepLiveDesign

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