FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Product-based/SZYBKI
Solution-based/Small Molecule Lead-opt/Ligand Entropy
Role-based/Computational Chemist
Task-based/Ligand Posing & Analysis
Description
FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI is a tool for evaluating the conformer free energy of compounds in solution. The conformer free energy is the free energy required to select a particular conformer out of the whole conformational ensemble in solution.
The minimal input into FreeForm Conformer Energies is a dataset of molecules in 1D (SMILES), 2D (SD, mol2), or 3D format.
Output from the FreeForm Conformer Energies floe is a conformational ensemble per input molecule, along with the associated free energies, and the probability of states for each conformer. The unit of free energy is kcal/mol.
Promoted Parameters
Title in user interface (promoted name)
FreeForm settings
Use input ensemble (use_inp_ens): Flag to use input ensemble conformers. Setting this to true would bypass any new conformer generation.
Type: boolean
Default: False
Choices: [True, False]
Include input conformer (include_input): Flag to include the input conformers in ensemble. Setting this to true would add the input conformers to the internally generated conformers.
Type: boolean
Default: False
Choices: [True, False]
Force Field (ff_type): Built-in force field model to be used.
Type: string
Default: sage
Choices: [‘mmff94s’, ‘parsley’, ‘sage’]
Custom FF File (ff): Custom smirnoff force field file. Entry in this field overrides any other force field selections
Type: file_in
Ionic state (ionic_state): Ionic state of molecules to be used
Type: string
Default: ph74
Choices: [‘ph74’, ‘uncharged’, ‘input’]