ptm-parameters 0.1.0

GROMOS force field parameters for protein post-translational modifications.

GROMOS force field parameters for protein post-translational modifications

The original set of parameters was published under CC BY 4.0 for GROMOS 45A3 and 54A7 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 and 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

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

• 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

• 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

• 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

License

Parameters are published under CC BY 4.0.

Authors

• Drazen Petrov - GitHub
• Christian Margreitter - GitHub
• Melanie Grandits
• Chris Oostenbrink - GitHub
• Bojan Žagrović - GitHub