OpenMM cubes and Floes 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
  • HydrationCube - Cube for hydrate a molecular system
  • SolvationCube - Cube for Solvate a molecular system in a given mixture solvent.
  • 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
  • YankSolvationFECube - YANK solvation free energy calculations
  • YankBindingFECube - 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_complex_prep.py - Assemble the complex starting from a set of ligands and a given receptor
  • floes/openmm_complex_prep_min.py - Assemble and minimize the complex starting from a set of ligands and a given receptor
  • 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
  • floes/openmm_MDprep_prod.py - Set up an OpenMM complex then minimize, warm up and equilibrate a system by using three equilibration stages. Finally a 2ns production simulation is performed
• 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.
  • floes/solvation_free_energy.py - Compute small molecule solvation free energies using YANK.
  • floes/binding_free_energy.py - Compute small molecule absolute binding free energies using YANK.

Local Installation

git clone git@github.com:oess/openmm_orion.git
cd openmm_orion

#Create a new local conda environment and install dependencies
conda create -n openmmorion python=3.5
source activate openmmorion
conda install -c omnia -c omnia/label/dev -c mobleylab -c OpenEye/label/Orion -c conda-forge openmm==7.1.1 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==0.18.0 oeommtools pymbar==3.0.3 networkx==1.11 

#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-0.2.181.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