Molecular fragmentation tool for quantum chemical torsion scan #open_force_field #RDKit

As many reader knows that quantum chemical(QC) calculations are useful and important to determine conformational distributions of small molecules. Because chemists design molecule with not only 2D information but also 3D information. However, computational cost of QC calculation is higher than molecular mechanics(MM) calculations. Last year, Prof. John D Chodera’s group published useful approach forContinue reading “Molecular fragmentation tool for quantum chemical torsion scan #open_force_field #RDKit”

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Conformer energy minimization with Openforcefield #OpenFF #RDKit

Last month, I posted topics about conformer generation code with rdkit. https://iwatobipen.wordpress.com/2021/01/31/generate-conformers-script-with-rdkit-rdkit-chemoinformatics/https://github.com/iwatobipen/rdk_confgen RDK_confgen can generate multiple conformers from molfile. This code generates conformers with MMFF94s forcefield. On the other hand recently open force field is very attractive package for these are I think. Fortunately OpenFF provides example code for conformer energy minimization as CLI tool.Continue reading “Conformer energy minimization with Openforcefield #OpenFF #RDKit”