Getting Started#

Installation#

Conda#

To install OpenAWSEM using Conda, execute the following command:

conda install -c conda-forge openawsem

Git#

This installation mode is recommended for users that want to contribute to the code and Wolynes lab members.

# Clone the awsem repository
git clone https://github.com/npschafer/openawsem.git
cd openawsem

# Create a new conda environment
conda create -n openawsem -c conda-forge --file requirements.txt
conda activate openawsem

# Install the package in editable mode
pip install -e .

Requirements#

STRIDE#

STRIDE is used for secondary structure prediction. Download and install STRIDE and add it to your PATH: https://webclu.bio.wzw.tum.de/stride/

mkdir stride
cd stride
wget https://webclu.bio.wzw.tum.de/stride/stride.tar.gz
tar -xvzf stride.tar.gz
make
echo 'export PATH=$PATH:'`pwd` >> ~/.bashrc

Note: If the webpage above becomes unavailable, please use an alternative repository like MDAnalysis/stride .

PSIBLAST#

Install psiblast using the distribution from bioconda:

conda install -c conda-forge -c bioconda blast

Alternatively Download and install psiblast and add it to your PATH: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

wget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/$(curl -s "https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/" | grep -o 'ncbi-blast-[0-9.]*+-x64-linux.tar.gz'| head -n 1)
tar -xvzf ncbi-*.tar.gz
cd ncbi*/bin
echo 'export PATH=$PATH:'`pwd` >> ~/.bashrc

PDB_SEQRES#

Download pdb_seqres.txt and put it in the cloned openawsem repository location

wget https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt
OPENAWSEM_LOCATION=$(python -c "import openawsem; print(openawsem.__location__)")
cp pdb_seqres.txt $OPENAWSEM_LOCATION/data

Predict_Property#

For secondary structure prediction from the fasta file OpenAWSEM can use “Predict_Property.sh -i {name}.fasta”. Install it from realbigws/Predict_Property. After installation, add Predict_property.sh to $PATH so it can be executed. For example add ‘export PATH=$PATH:/Users/weilu/Research/Build/Predict_Property/’ inside the ~/.bash_profile file.

Example#

Simulation of the amino terminal domain of Phage 434 repressor (1r69)

Activate the OpenMM Environment:

Activate the required environment for running simulations:
```
source activate openmm
```
Set Up the Simulation Folder:

Create a simulation folder using the awsem_create command. The command will automatically download the corresponding pdb:
```
awsem_create 1r69 --frag
```
Alternatively, if you have the 1r69.pdb file:
```
awsem_create 1r69.pdb --frag
```

Modify the forces_setup.py

The forces_setup.py script 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.

Original:

# 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 the awsem_run command, 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_run 1r69 --platform CPU --steps 1e5 --tempStart 800 --tempEnd 200 -f forces_setup.py
```
Compute Energy and Q:

Analyze the simulation results and redirect the output to info.dat:
```
awsem_analyze 1r69 > info.dat
```
Run 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.py 1r69 --platform CPU --steps 1e5 --tempStart 800 --tempEnd 200 -f forces_setup.py
./mm_analyze.py 1r69 > energy.dat
```