Update of openmm_runner #moleculardynamics #TeachOpenCADD #rdkit #openmm #chemoinformatics

Some days ago, I made a post about openmm_runner. Previous code can’t calculate MD which contains metal ion such as Mg2+. I wonder that does openmm can handle metal ion. I asked the question in the openmm community and could get the answer ;) I know that ‘Amber14 includes parameters for Mg2+ as well asContinue reading “Update of openmm_runner #moleculardynamics #TeachOpenCADD #rdkit #openmm #chemoinformatics”

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Make mdtools for openmm #moleculardynamics #TeachOpenCADD #rdkit #openmm #chemoinformatics

As chemoinformatitians know that TeachOpenCADD(TOCADD) is one of the really useful site for learning in-silico drug discovery pipeline. It supports wide range of chemoinformatics not only LBDD but also SBDD. New version of TOCADD supports Molecular dynamics(MD) tutorial with openmm. The talktorial T019 and T020 show how to run and analyse MD with openmm andContinue reading “Make mdtools for openmm #moleculardynamics #TeachOpenCADD #rdkit #openmm #chemoinformatics”

Example usage of psi4-openmm-interface #Psi4 #OpenMM #RDKit

Molecular dynamics and Quantum Chemistry are important tools for CADD. I have interested in these topics and OpenMM and Psi4 are nice tool to handing MD and QM. Today I tried to use psi4-openmm-interface which allows passing of molecular systems between each program. I reviewed test script and found that the package pass the moleculeContinue reading “Example usage of psi4-openmm-interface #Psi4 #OpenMM #RDKit”