| Name | openawsem JSON |
| Version |
1.1.1
JSON |
| download |
| home_page | https://openawsem.org/ |
| Summary | Calculates single residue frustration, and mutational frustration of proteins. |
| upload_time | 2023-11-04 20:03:59 |
| maintainer | |
| docs_url | None |
| author | Carlos Bueno |
| requires_python | >=3.8 |
| license | MIT |
| keywords |
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# OpenAWSEM
## An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM
OpenAWSEM 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.
## Installation
### Conda
To install OpenAWSEM using Conda, execute the following command:
```bash
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.
```bash
#Clone the awsem repository
git clone https://github.com/cabb99/openawsem.git
cd openawsem
# Create a new conda environment
conda create -n openawsem --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/
```bash
wget https://webclu.bio.wzw.tum.de/stride/stride.tar.gz
tar -xvzf stride.tar.gz
cd stride
make
echo 'export PATH=$PATH:'`pwd` >> ~/.bashrc
```
### PSIBLAST
Install psiblast using the distribution from bioconda:
```
conda install -c bioconda blast
```
Alternatively Download and install psiblast and add it to your PATH:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
```bash
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/$(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=$PATH:'`pwd` >> ~/.bashrc
```
### PDB_SEQRES.txt
* Download pdb_seqres.txt and put it in the cloned openawsem repository location
```
wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt
OPENAWSEM_LOCATION=$(python -c "import openawsem; print(openawsem.__location__)")
cp pdb_seqres.txt $OPENAWSEM_LOCATION/data
```
## Configuration
OpenAWSEM 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/topology
```
## Example
Simulation of the amino terminal domain of Phage 434 repressor (1r69)
1. **Activate the OpenMM Environment:**
Activate the required environment for running simulations.
```bash
source activate openmm
```
2. **Set Up the Simulation Folder:**
Create a simulation folder using the `awsem_create` command. The awsem_create command will automatically download the corresponding pdb.
```bash
awsem_create 1r69 --frag
```
Alternatively, if you have the `1r69.pdb` file:
```bash
awsem_create 1r69.pdb --frag
```
3. **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.
```python
# 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:
```python
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),
```
3. **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.
```bash
awsem_run 1r69 --platform CPU --steps 1e5 --tempStart 800 --tempEnd 200 -f forces_setup.py
```
4. **Compute Energy and Q:**
Analyze the simulation results and redirect the output to `info.dat`.
```bash
awsem_analyze 1r69 > info.dat
```
5. **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:
```bash
./mm_run.py 1r69 --platform CPU --steps 1e5 --tempStart 800 --tempEnd 200 -f forces_setup.py
./mm_analyze.py 1r69 > energy.dat
```
## Notes:
For small proteins, the LAMMPS version may be faster than OpenAWSEM, especially if a GPU is unavailable. Consider using http://awsem-md.org for such cases.
A quick check of the stability of a protein in AWSEM can be done using the frustratometer server http://frustratometer.qb.fcen.uba.ar/
## Data availability
Data related to the paper "OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations" is available at https://app.globus.org/file-manager?origin_id=b4cef8ce-7773-4016-8513-829f388f7986&origin_path=%2FopenAWSEM_data%2F
## Citation
Please 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
Raw data
{
"_id": null,
"home_page": "https://openawsem.org/",
"name": "openawsem",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": "",
"keywords": "",
"author": "Carlos Bueno",
"author_email": "carlos.bueno@rice.edu",
"download_url": "https://files.pythonhosted.org/packages/31/46/d8ef9e18e71f34afb9df43fcb6b6822014c46075f6b1be9eaf435db243a7/openawsem-1.1.1.tar.gz",
"platform": null,
"description": "# OpenAWSEM\n## An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM\n\nOpenAWSEM 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.\n\n## Installation\n\n### Conda\n\nTo install OpenAWSEM using Conda, execute the following command:\n\n```bash\nconda install -c conda-forge openawsem\n```\n\n### Git\n\nThis installation mode is recommended for users that want to contribute to the code and Wolynes lab members.\n\n```bash\n#Clone the awsem repository\ngit clone https://github.com/cabb99/openawsem.git\ncd openawsem\n\n# Create a new conda environment\nconda create -n openawsem --file requirements.txt\nconda activate openawsem\n\n# Install the package in editable mode\npip install -e .\n```\n\n## Requirements\n\n### STRIDE\nSTRIDE is used for secondary structure prediction. \nDownload and install STRIDE and add it to your PATH:\nhttps://webclu.bio.wzw.tum.de/stride/\n```bash\nwget https://webclu.bio.wzw.tum.de/stride/stride.tar.gz\ntar -xvzf stride.tar.gz\ncd stride\nmake\necho 'export PATH=$PATH:'`pwd` >> ~/.bashrc\n```\n\n### PSIBLAST \nInstall psiblast using the distribution from bioconda:\n\n```\nconda install -c bioconda blast\n```\n\nAlternatively Download and install psiblast and add it to your PATH: \nftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/\n\n```bash\nwget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/$(curl -s \"https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/\" | grep -o 'ncbi-blast-[0-9.]*+-x64-linux.tar.gz'| head -n 1)\ntar -xvzf ncbi-*.tar.gz\ncd ncbi*/bin\necho 'export PATH=$PATH:'`pwd` >> ~/.bashrc\n```\n\n### PDB_SEQRES.txt\n* Download pdb_seqres.txt and put it in the cloned openawsem repository location\n```\nwget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt\nOPENAWSEM_LOCATION=$(python -c \"import openawsem; print(openawsem.__location__)\")\ncp pdb_seqres.txt $OPENAWSEM_LOCATION/data\n\n```\n\n## Configuration\nOpenAWSEM allows users to configure data storage paths. To do this:\n\nCreate a .awsem directory in your home folder.\nInside .awsem, create a configuration file named config.ini to specify data paths. \nThe default paths point to the local data directory inside the OpenAWSEM module.\nExample config.ini:\n\n```\n[Data Paths]\nblast = /home/USER/data/database/cullpdb_pc80_res3.0_R1.0_d160504_chains29712\ngro = /home/USER/data/Gros\npdb = /home/USER/data/PDBs\nindex = /home/USER/data/Indices\npdbfail = /home/USER/data/notExistPDBsList\npdbseqres = /home/USER/data/pdb_seqres.txt\ntopology = /home/USER/topology\n```\n\n## Example\nSimulation of the amino terminal domain of Phage 434 repressor (1r69)\n\n1. **Activate the OpenMM Environment:**\n Activate the required environment for running simulations.\n ```bash\n source activate openmm\n ```\n\n2. **Set Up the Simulation Folder:**\n Create a simulation folder using the `awsem_create` command. The awsem_create command will automatically download the corresponding pdb.\n ```bash\n awsem_create 1r69 --frag\n ```\n Alternatively, if you have the `1r69.pdb` file:\n ```bash\n awsem_create 1r69.pdb --frag\n ```\n\n3. **Modify the forces_setup.py**\n\n The `forces_setup.py` script determines which force (energy) terms are included in the simulation. \n To activate the fragment memory term uncomment the fragment memory term and comment the single memory term.\n ```python\n # templateTerms.fragment_memory_term(oa, frag_file_list_file=\"./frags.mem\", npy_frag_table=\"./frags.npy\", UseSavedFragTable=True),\n templateTerms.fragment_memory_term(oa, frag_file_list_file=\"./single_frags.mem\", npy_frag_table=\"./single_frags.npy\", UseSavedFragTable=False),\n ```\n It should look like this:\n ```python\n templateTerms.fragment_memory_term(oa, frag_file_list_file=\"./frags.mem\", npy_frag_table=\"./frags.npy\", UseSavedFragTable=False),\n # templateTerms.fragment_memory_term(oa, frag_file_list_file=\"./single_frags.mem\", npy_frag_table=\"./single_frags.npy\", UseSavedFragTable=False),\n ```\n3. **Run the Simulation:**\n Execute the simulation using the `awsem_run` command, specifying the platform, number of steps, and start and end temperatures for the annealing simulation.\n As an example we are running 1e5 steps, but it is common to run from 5 to 30 million steps in a single run.\n \n ```bash\n awsem_run 1r69 --platform CPU --steps 1e5 --tempStart 800 --tempEnd 200 -f forces_setup.py\n ```\n\n4. **Compute Energy and Q:**\n Analyze the simulation results and redirect the output to `info.dat`.\n ```bash\n awsem_analyze 1r69 > info.dat\n ```\n\n5. **Run Local Scripts (Optional):**\n The scripts are copied to the project folder and can be modified as needed. To run the local scripts, use the following commands:\n ```bash\n ./mm_run.py 1r69 --platform CPU --steps 1e5 --tempStart 800 --tempEnd 200 -f forces_setup.py\n ./mm_analyze.py 1r69 > energy.dat\n ```\n\n## Notes:\nFor small proteins, the LAMMPS version may be faster than OpenAWSEM, especially if a GPU is unavailable. Consider using http://awsem-md.org for such cases.\nA quick check of the stability of a protein in AWSEM can be done using the frustratometer server http://frustratometer.qb.fcen.uba.ar/\n\n## Data availability\nData related to the paper \"OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations\" is available at https://app.globus.org/file-manager?origin_id=b4cef8ce-7773-4016-8513-829f388f7986&origin_path=%2FopenAWSEM_data%2F\n\n## Citation\nPlease cite the following paper when using OpenAWSEM:\nLu, 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\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Calculates single residue frustration, and mutational frustration of proteins.",
"version": "1.1.1",
"project_urls": {
"Homepage": "https://openawsem.org/"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "a87b26764a63e31f0cab4fbf469aa603f2d111cbbd665c493035dfc555cc1127",
"md5": "de1cca5ac262d057754fdb166f86a6f8",
"sha256": "3fe3db7c1ad8d95da3a0e29ef378cf90c68675bddbab6007969ab211aad60594"
},
"downloads": -1,
"filename": "openawsem-1.1.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "de1cca5ac262d057754fdb166f86a6f8",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 13788338,
"upload_time": "2023-11-04T20:03:56",
"upload_time_iso_8601": "2023-11-04T20:03:56.468904Z",
"url": "https://files.pythonhosted.org/packages/a8/7b/26764a63e31f0cab4fbf469aa603f2d111cbbd665c493035dfc555cc1127/openawsem-1.1.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "3146d8ef9e18e71f34afb9df43fcb6b6822014c46075f6b1be9eaf435db243a7",
"md5": "3783fa66a859f0306ec73304e018b434",
"sha256": "0870ee19431d1977cd85f1a000b8984416cf78f02d15b8292e13fb648df4cc5a"
},
"downloads": -1,
"filename": "openawsem-1.1.1.tar.gz",
"has_sig": false,
"md5_digest": "3783fa66a859f0306ec73304e018b434",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 13703169,
"upload_time": "2023-11-04T20:03:59",
"upload_time_iso_8601": "2023-11-04T20:03:59.859454Z",
"url": "https://files.pythonhosted.org/packages/31/46/d8ef9e18e71f34afb9df43fcb6b6822014c46075f6b1be9eaf435db243a7/openawsem-1.1.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-04 20:03:59",
"github": false,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"lcname": "openawsem"
}
