Automated CG-to-AA workflow for protein condensate simulations
Project description
CondenSimAdapter
CondenSimAdapter is an automated workflow for protein condensate simulations, covering the main stages from CG to AA.
Installation
1. Create a conda environment
conda create -n conden python=3.11 -y
conda activate conden
2. Download and install dependency
Download the zip from GitHub webpage or run:
wget https://github.com/hanlab-computChem/CondenSimAdapter/archive/refs/heads/main.zip
Unzip and enter the directory:
unzip CondenSimAdapter-master.zip
cd CondenSimAdapter-master
Run the installation script:
bash install.sh
3. Install CondenSimAdapter
pip install .
4. For COCOMO multidomain protein simulations (Optional)
pip install git+https://github.com/feiglab/mdsim.git
pip install numpy==1.26.4 mdtraj==1.11.0
Note: mdsim claims it needs higher dependency versions, but downgrading numpy and mdtraj to the versions above does not affect COCOMO simulations.
5. Run test
python -m pytest
6. Run with CondenSimAdapter command adapter
adapter -h
Requirements
-
Python = 3.11
-
CUDA >= 12.1
-
GROMACS >= 2023 (install it yourself)
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