dan-burns / openawsem

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

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

• Install conda or miniconda: https://conda.io/en/latest/miniconda.html
• Create an openmm environment that includes the necessary Python packages.

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

• Note 2: If you dont have GPU avaliable, you might want to consider using http://awsem-md.org. For small proteins, the LAMMPS version could be faster than openAWSEM.

• Note 3: Due to the size limitation, the data for the paper OpenAWSEM with Open3SPN2: a fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations is stored in https://app.globus.org/file-manager?origin_id=b4cef8ce-7773-4016-8513-829f388f7986&origin_path=%2FopenAWSEM_data%2F

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