Package: openawsem
OpenAWSEMAn implementation of the AWSEM coarse-grained protein folding forcefield in OpenMMOpenAWSEM is an implementation of the AWSEM (Associative memory, Water-mediated Structure, and Energy Model) coarse-grained protein forcefield designed for use with the OpenMM simulation toolkit.InstallationCondaTo install OpenAWSEM using Conda, execute the following command:condainstall-cconda-forgeopenawsemGitThis installation mode is recommended for users that want to contribute to the code and Wolynes lab members.#Clone the awsem repositorygitclonehttps://github.com/cabb99/openawsem.gitcdopenawsem# Create a new conda environmentcondacreate-nopenawsem--filerequirements.txt
condaactivateopenawsem# Install the package in editable modepipinstall-e.RequirementsSTRIDESTRIDE is used for secondary structure prediction.
Download and install STRIDE and add it to your PATH:https://webclu.bio.wzw.tum.de/stride/wgethttps://webclu.bio.wzw.tum.de/stride/stride.tar.gz
tar-xvzfstride.tar.gzcdstride
makeecho'export PATH=$PATH:'`pwd`>>~/.bashrcPSIBLASTInstall psiblast using the distribution from bioconda:conda install -c bioconda blastAlternatively Download and install psiblast and add it to your PATH:ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/wgethttps://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/$(curl-s"https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/"|grep-o'ncbi-blast-[0-9.]*+-x64-linux.tar.gz'|head-n1)tar-xvzfncbi-*.tar.gzcdncbi*/binecho'export PATH=$PATH:'`pwd`>>~/.bashrcPDB_SEQRES.txtDownload pdb_seqres.txt and put it in the cloned openawsem repository locationwget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt
OPENAWSEM_LOCATION=$(python -c "import openawsem; print(openawsem.__location__)")
cp pdb_seqres.txt $OPENAWSEM_LOCATION/dataConfigurationOpenAWSEM allows users to configure data storage paths. To do this:Create a .awsem directory in your home folder.
Inside .awsem, create a configuration file named config.ini to specify data paths.
The default paths point to the local data directory inside the OpenAWSEM module.
Example config.ini:[Data Paths]
blast = /home/USER/data/database/cullpdb_pc80_res3.0_R1.0_d160504_chains29712
gro = /home/USER/data/Gros
pdb = /home/USER/data/PDBs
index = /home/USER/data/Indices
pdbfail = /home/USER/data/notExistPDBsList
pdbseqres = /home/USER/data/pdb_seqres.txt
topology = /home/USER/topologyExampleSimulation of the amino terminal domain of Phage 434 repressor (1r69)Activate the OpenMM Environment:Activate the required environment for running simulations.sourceactivateopenmmSet Up the Simulation Folder:Create a simulation folder using theawsem_createcommand. The awsem_create command will automatically download the corresponding pdb.awsem_create1r69--fragAlternatively, if you have the1r69.pdbfile:awsem_create1r69.pdb--fragModify the forces_setup.pyTheforces_setup.pyscript determines which force (energy) terms are included in the simulation.
To activate the fragment memory term uncomment the fragment memory term and comment the single memory term.# templateTerms.fragment_memory_term(oa, frag_file_list_file="./frags.mem", npy_frag_table="./frags.npy", UseSavedFragTable=True),templateTerms.fragment_memory_term(oa,frag_file_list_file="./single_frags.mem",npy_frag_table="./single_frags.npy",UseSavedFragTable=False),It should look like this:templateTerms.fragment_memory_term(oa,frag_file_list_file="./frags.mem",npy_frag_table="./frags.npy",UseSavedFragTable=False),#  templateTerms.fragment_memory_term(oa, frag_file_list_file="./single_frags.mem", npy_frag_table="./single_frags.npy", UseSavedFragTable=False),Run the Simulation:Execute the simulation using theawsem_runcommand, specifying the platform, number of steps, and start and end temperatures for the annealing simulation.
As an example we are running 1e5 steps, but it is common to run from 5 to 30 million steps in a single run.awsem_run1r69--platformCPU--steps1e5--tempStart800--tempEnd200-fforces_setup.pyCompute Energy and Q:Analyze the simulation results and redirect the output toinfo.dat.awsem_analyze1r69>info.datRun Local Scripts (Optional):The scripts are copied to the project folder and can be modified as needed. To run the local scripts, use the following commands:./mm_run.py1r69--platformCPU--steps1e5--tempStart800--tempEnd200-fforces_setup.py
./mm_analyze.py1r69>energy.datNotes:For small proteins, the LAMMPS version may be faster than OpenAWSEM, especially if a GPU is unavailable. Consider usinghttp://awsem-md.orgfor such cases.
A quick check of the stability of a protein in AWSEM can be done using the frustratometer serverhttp://frustratometer.qb.fcen.uba.ar/Data availabilityData related to the paper "OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations" is available athttps://app.globus.org/file-manager?origin_id=b4cef8ce-7773-4016-8513-829f388f7986&origin_path=%2FopenAWSEM_data%2FCitationPlease cite the following paper when using OpenAWSEM:
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