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