GoCa

Generate structure-based coarse-grained protein models for molecular dynamics simulations!
The GoCa program can also be used via the luiswalter.dev/GoCa webserver.

Installation

We use Make to build the binary.

git clone git@github.com:daandtu/GoCa.git
cd GoCa
git submodule init # Fetch dependencies
git submodule update
make

Usage

Copy the default configuration file default.ini to your target directory and modify it according to your needs.
Execute the program binary to generate a topology and coordinate file. Pass the previously created configuration file as a command line argument. If no configuration file is specified, the script searches for a file named GoCa.ini.
```
./path_to_this_repository/GoCa configuration.ini
```
Use the topology and coordinate files for your simulation (for example, with this GROMACS configuration).

Tests

To run the provided test, install pytest and run from the main directory

python3 -m pytest tests

About

Generate simulation files for structure-based coarse-grained protein models.

Languages

Language:Jupyter Notebook 48.4%Language:C++ 33.8%Language:Python 17.1%Language:Shell 0.5%Language:Makefile 0.2%