Parameters
ViennaPTM uses dedicated GROMOS force-field parameters for post-translationally modified amino acids. These parameters are required for GROMACS energy minimization in the webserver and for molecular dynamics simulations of modified structures prepared with ViennaPTM.
The parameter sets cover GROMOS 45A3, 54A7, and 54A8, including extensions for phosphorylated and other charged PTMs in the 54A8 force field. They are published under CC BY 4.0.
Download & installation
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GitHub repository
Source files, GROMACS and GROMOS parameter directories, and usage instructions for integrating the parameters into your simulation workflow.
github.com/viennaptm/ptm_parameters -
PyPI package
Install the parameters as a Python package for use with ViennaPTM and related tooling:
pypi.org/project/ptm-parameterspip install ptm-parameters
For citation information, see Resources → Papers. For ViennaPTM usage and API documentation, see the Backend Wiki.