PlatformTestCubes/- simple example cube for testing available OpenMM PlatformTestCubesPlatformTestCube- Checks available OpenMM PlatformsBenchmarkCube- Benchmark available OpenMM Platforms
LigPrepCubes/- Cubes for preparing moleculesLigChargeCube- Charges ligands by using the ELF10 charge methodFREDDocking- Dock MCMols using FRED to a prepared receptor
ComplexPrepCubesReader- Protein Reader CubeSplitter- Splits bio-molecular system into: protein, ligand, water and excipientsSolvationCube- Solvates the molecular system.ComplexPrep- Assembles complex made of solvated system and ligandsForceFieldPrep- Parameterizes the system given a forcefield.
OpenMMCubes/- OpenMM utility cubesOpenMMminimizeCube- Minimize the protein:ligand complex.OpenMMnvtCube- NVT simulation of the protein:ligand complexOpenMMnptCube- NPT simulation of the protein:ligand complex.
YankCubes/- YANK cubesYankHydrationCube- YANK hydration free energy calculationsYankBindingCube- YANK absolute binding free energy calculations
- Testing Floes:
floes/platformTest.py- Check available OpenMM Platformsfloes/openmm_benchmarking.py- Performs Benchmarking upon all available Platforms.
- OpenMM Floes:
floes/openmm_MDminimize.py- Minimize an OpenMM-ready solvated complexfloes/openmm_MDnpt.py- NPT simulation of an OpenMM-ready solvated complexfloes/openmm_MDnvt.py- NVT simulation of an OpenMM-ready solvated complexfloes/openmm_MDprep.py- Set up an OpenMM complex then minimize, warm up and equilibrate a system by using three equilibration stagesfloes/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.
git clone git@github.com: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