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OpenAWSEM

An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM

The OpenAWSEM code is currently being tested. Use at your own risk. And let us know what you find. :-)

Installation

  • Clone openawsem repository
git clone https://github.com/npschafer/openawsem.git
  • Download and install STRIDE and put it in your PATH: http://webclu.bio.wzw.tum.de/stride/
  • Download and install psiblast and put it in your PATH: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
  • Download pdb_seqres.txt and put it in the cloned openawsem repository location
wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt
conda create -n openmm python=3.6 biopython matplotlib numpy pandas 
  • Set OPENAWSEM_LOCATION environment variable (the location where you cloned this Github repository).
export OPENAWSEM_LOCATION='/YOUR/OPENAWSEM/DIRECTORY/'
  • Activate the openmm environment.
source activate openmm
  • Install additional python packages
conda install -c omnia -c conda-forge openmm pdbfixer mdtraj 

Example

Simulate Phage 434 repressor amino terminal domain (1r69)

  • Activate the openmm environment.
source activate openmm
  • Setup simulation folder:
python YOUR_OPENAWSEM_LOCATION/mm_create_project.py 1r69 --frag
  • Or if you already have 1r69.pdb:
python YOUR_OPENAWSEM_LOCATION/mm_create_project.py PATH_TO_YOUR_PDB/1r69.pdb --frag
  • Run the simulation:
python mm_run.py 1r69 --platform CPU --steps 1e5 --tempStart 800 --tempEnd 200 -f forces_setup.py
  • Note:

forces_setup.py controls which force(energy) term will be included in the simulation.

  • Compute energy and Q:
python mm_analysis.py 1r69 > energy.dat

Citation

Lu, W., Bueno, C., Schafer, N. P., Moller, J., Jin, S., Chen, X., ... & Wolynes, P. G. (2021). OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLoS computational biology, 17(2), e1008308. https://doi.org/10.1371/journal.pcbi.1008308

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An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM

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