Metadata-Version: 2.4
Name: ptm_parameters
Version: 0.1.0
Summary: GROMOS force field parameters for protein post-translational modifications.
Author-email: Drazen Petrov <durozlikovski@gmail.com>, Christian Margreitter <christian.margreitter@gmail.com>, Melanie Grandits <melanie.grandits@univie.ac.at>, Chris Oostenbrink <chris.oostenbrink@boku.ac.at>, Bojan Žagrović <bojan.zagrovich@univie.ac.at>
Maintainer-email: Drazen Petrov <durozlikovski@gmail.com>, Christian Margreitter <christian.margreitter@gmail.com>
License-Expression: CC-BY-4.0
Project-URL: Homepage, https://viennaptm.univie.ac.at
Project-URL: Repository, https://github.com/viennaptm/ptm_parameters
Keywords: Post-translational modifications,Force field,ptm_parameters,ptm,parameters,python,python-packages,semantic-versions
Classifier: Development Status :: 5 - Production/Stable
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pydantic>=2
Provides-Extra: build
Requires-Dist: twine; extra == "build"
Requires-Dist: build; extra == "build"
Dynamic: license-file

# GROMOS force field parameters for protein post-translational modifications

The original set of parameters was published under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) for [GROMOS 45A3 and 54A7](https:///doi.org/10.1371/journal.pcbi.1003154) parameter sets, compatible with the `GROMACS` molecular simulation package.

This repository includes the original set and extends to `GROMOS` 54A8 parameter set, including additional modifications and compatibility with `GROMOS` and `GROMACS` simulation packages.

## Usage
Refer to individual instructions for [GROMOS](ptm_parameters/GROMOS) and [GROMACS](ptm_parameters/GROMACS).

## How to cite

Please cite:

1. Petrov D., Margreitter C., Grandits M., Oostenbrink C. and Zagrovic B.  
   *A systematic framework for molecular dynamics simulations of protein post-translational modifications.*  
   *PLoS Comput Biol.* 2013;9:e1003154.  
   [DOI: 10.1371/journal.pcbi.1003154](https://doi.org/10.1371/journal.pcbi.1003154)

Additional citations depending on usage:

- **If using the 54A8 parameter set:**

  Reif M., Hünenberger P. and Oostenbrink C.  
  *New interaction parameters for charged amino acid side chains in the GROMOS force field.*  
  *J. Chem. Theory Comput.* 2012;8:3705–3723.  
  [DOI: 10.1021/ct300156h](https://doi.org/10.1021/ct300156h)

- **If using the 54A7 parameter set:**

  Schmid N., Eichenberger A.P., Choutko A., Riniker S., Winger M., Mark A.E. and van Gunsteren W.F.  
  *Definition and testing of the GROMOS force-field versions 54A7 and 54B7.*  
  *Eur Biophys J.* 2011;40:843–856.  
  [DOI: 10.1007/s00249-011-0700-9](https://doi.org/10.1007/s00249-011-0700-9)

- **If using phosphorylated residues with 54A8:**

  Margreitter C., Grandits M. and Oostenbrink C.  
  *Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field.*  
  *J. Comput. Chem.* 2017;38:714–720.  
  [DOI: 10.1002/jcc.24733](https://doi.org/10.1002/jcc.24733)

- **If the initial protein structure was generated using ViennaPTM:**

  Margreitter C., Petrov D. and Zagrovic B.  
  *Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications.*  
  *Nucleic Acids Res.* 2013;41(W1):W422–W426.  
  [DOI: 10.1093/nar/gkt416](https://doi.org/10.1093/nar/gkt416)

## License
Parameters are published under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).

## Authors
- **Drazen Petrov** - [GitHub](https://github.com/drazen-petrov)
- **Christian Margreitter** - [GitHub](https://github.com/CMargreitter)  
- **Melanie Grandits**
- **Chris Oostenbrink** - [GitHub](https://github.com/oostenbrink)
- **Bojan Žagrović** - [GitHub](https://github.com/bojanzagrovic)



