CHARMM36M Force Field Parameters for the Thioester Bond between Cysteine and Glycine

This dataset provides CHARMM36M force field parameters for the thioester bond that connects the side chain of a cysteine residue to the carbonyl group of a C-terminal glycine residue. The parameters are provided in GROMACS format. Additional setting files for pdb2gmx are also provided. A short tutorial demonstrates how to patch the CHARMM36M force field and use the parameters.

This new version incorporates changes made to the specbond.dat file in the GROMACS 2025 release. These changes fixed a bug in the pdb2gmx tool that previously generated incomplete thioester topologies, necessitating manual edits. GROMACS 2025 does not require these edits.  

The force field parameters were developed for simulations of the Ubc6 ubiquitin complex but can be used with any comparable system.

Details about the parameterization are provided in:

Swarnkar, Anuruti, Florian Leidner, Ashok K. Rout, Sofia Ainatzi, Claudia C. Schmidt, Stefan Becker, Henning Urlaub, Christian Griesinger, Helmut Grubmüller, and Alexander Stein. "Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes." The EMBO Journal (2024): 1-35.

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