shunsunsun / dock-md-fep

A three-in-one workflow, Dock with Autodock, MD with OpenMM, FEP with OpenMM/yank

Restart the simulation

Open the Dock-MD-FEP-restart.ipynb, after pasting the working directory path of last simulation. Import drive mannually, then run all the other cells at one time.

Dock-MD-FEP

This notebook only requires four strings, then all the rest is handled by the code itself.

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Docking, Molecular dynamic(MD), and Free energy perturbation (FEP) are important modelling methods in medicinal chemistry.

This Jupyter notebook shows how to run a Three-in-one simulation, i.e., docking, MD and FEP, with freely available GPU(and CPU) from Google Colab.

default parameters

-- MD , all MD input use Amber Gaff2 force field to deal with small molecule.

MD 0 , equilibration 0.5 ns, production 1.0 ns. OpenMM as simulation engine.

MD 1, equilibration 1.0 ns, production 2.0 ns. OpenMM as simulation engine.

Dock, gnina, --exaustiveness=200. The best pose with docking score and best CNN score was carried on to FEP

FEP, stop simulaiton when reaching error < 0.1 KT, Simulation engine OpenMM with Yank python library.

Free energy of binding(benzene) : -11.229 +- 0.352 kT (-6.694 +- 0.210 kcal/mol)