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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Run MD simulation with cloud resource #openmm #google_colab

Molecular dynamics (MD) simulation is one of the useful approach for estimating protein-ligand interaction. However, computational cost of MD simulation is high, so large computational resource is required when we run the large scale MD simulation. On the other hand, now we can use freely available could computational resource such as Google colab. It’s notContinue reading “Run MD simulation with cloud resource #openmm #google_colab”

Install mdfptools #Chemoinformatics #RDKit #memo

I heard many exciting presentation at virtual meeting of ‘3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry’. And I had interest about MDFP (molecular dynamics Finger Print). MDFP can analyze molecular flexibility and solvent accessible surface are (SASA) etc. They are important parameters for permeability, p-gp and other molecular properties. In the following article combinationContinue reading “Install mdfptools #Chemoinformatics #RDKit #memo”