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MD simulations

PC Pierre Cazade

Last updated date: Jun 20, 2025 Views: 8 Forks: 0

original An abbreviated version of this protocol was published in Science Advances in Nov, 2021
Modulating the pro-apoptotic activity of cytochrome c at a biomimetic electrified interface
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We are using CHARMM forcefield. For heme c, the parameters come from a different research group. Files with these parameters have been attached. Heme c covalently binds to two cysteines. There are two sets of parameters depending on heme c oxidation state (II or III).

 

For the bc1 complex, aside from cytochrome c1, all other hemes are heme b for which CHARMM provides standard parameters found in the merged.rtp file.

Related files

zip charmm36-pc-dt-ms.ff.zip download
Copyright: © 2025 The Author(s); This is an open-access article under the CC BY-NC license (https://creativecommons.org/licenses/by-nc/4.0/).
How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Cazade, P(2025). MD simulations. Bio-protocol Preprint. bio-protocol.org/prep2830.
  2. Gamero-Quijano, A., Bhattacharya, S., Cazade, P., Molina-Osorio, A. F., Beecher, C., Djeghader, A., Soulimane, T., Dossot, M., Thompson, D., Herzog, G. and Scanlon, M. D.(2021). Modulating the pro-apoptotic activity of cytochrome c at a biomimetic electrified interface. Science Advances 7(45). DOI: 10.1126/sciadv.abg4119

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