How can I simulate disulfide bond formation using MD?

Mohammed Nooraldeen Al-Qattan @Mohammed-Al-Qattan

12 May 2014 1 7K Report

Although it is familiar in molecular biology, I could not found it in literature.

Using QM/MM is known to stimulate bond formation and breaking, however, how to drag this reaction to take place in AMBER.

If I am to use the simplified bond formation and breaking force field (Reaxff), how to incorporate it into Amber?

Peng Lian

Not sure in AMBER. In CHARMM, you can use the reaction coordinate driving method to guide your reactions. If you plan to do it with semi-empirical method for QM region calculation, you can use SCC-DFTB/MM.

For your reference,

Article Catalytic mechanism and origin of high activity of cellulase...

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