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README.md

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OpenMM cubes and workfloes for Orion

Cube sets

  • PlatformTestCubes/ - simple example cube for testing available OpenMM PlatformTestCubes
    • PlatformTestCube- Checks available OpenMM Platforms
    • BenchmarkCube - Benchmark available OpenMM Platforms
  • LigPrepCubes/ - Cubes for preparing molecules
    • LigChargeCube- Charges ligands by using the ELF10 charge method
    • FREDDocking - Dock MCMols using FRED to a prepared receptor
  • ComplexPrepCubes
    • Reader - Protein Reader Cube
    • Splitter- Splits bio-molecular system into: protein, ligand, water and excipients
    • SolvationCube - Solvates the molecular system.
    • ComplexPrep - Assembles complex made of solvated system and ligands
    • ForceFieldPrep - Parameterizes the system given a forcefield.
  • OpenMMCubes/ - OpenMM utility cubes
    • OpenMMminimizeCube - Minimize the protein:ligand complex.
    • OpenMMnvtCube - NVT simulation of the protein:ligand complex
    • OpenMMnptCube- NPT simulation of the protein:ligand complex.
  • YankCubes/ - YANK cubes
    • YankHydrationCube - YANK hydration free energy calculations
    • YankBindingCube - YANK absolute binding free energy calculations

Workfloes

  • Testing Floes:
    • floes/platformTest.py - Check available OpenMM Platforms
    • floes/openmm_benchmarking.py - Performs Benchmarking upon all available Platforms.
  • OpenMM Floes:
    • floes/openmm_MDminimize.py - Minimize an OpenMM-ready solvated complex
    • floes/openmm_MDnpt.py - NPT simulation of an OpenMM-ready solvated complex
    • floes/openmm_MDnvt.py - NVT simulation of an OpenMM-ready solvated complex
    • floes/openmm_MDprep.py - Set up an OpenMM complex then minimize, warm up and equilibrate a system by using three equilibration stages
    • floes/openmm_MDprod.py - Run an unrestrained NPT simulation at 300K and 1atm
  • YANK Floes
    • floes/yank_hydration.py - Compute small molecule hydration free energies using YANK.
    • floes/yank_binding.py - Compute small molecule absolute binding free energies using YANK.
  • Other Floes:
    • floes/openmm_complex_setup.py - Setup the protein:ligand complex from PDBs.

Local Installation

git clone [email protected]:oess/openmm_orion.git
cd openmm_orion

#Create a new local conda environment and install dependencies
conda create -c omnia -c omnia/label/dev -c mobleylab -c nividic -n dev python=3.5 openmm==7.1.0rc1 openmoltools==0.8.1 ambermini==16.16.0 parmed==2.7.3 pdbfixer==1.4 openforcefield==0.0.2 smirff99frosst==1.0.5 alchemy==1.2.3 yank==0.15.2 oeommtools==0.0.1
source activate dev

#Install the OpenEye-floe package and toolkits
pip install -i https://pypi.anaconda.org/OpenEye/simple OpenEye-toolkits
pip install --pre --extra-index-url https://pypi.anaconda.org/OpenEye/channel/beta/simple OpenEye-oenotebook
pip install OpenEye-floe-0.2.158.tar.gz

#Install the main OpenMM Orion Floes
python setup.py develop

# Run the tests.
py.test -v -s PlatformTestCubes
py.test -v -s LigPrepCubes
py.test -v -s ComplexPrepCubes
py.test -v -s -m "not slow" OpenMMCubes