Hello,
I have a question regarding a steered QM experiment I am working on. I have a ligand within the active site of an enzyme containing a heme. The ligand contains a thiophene moiety which should undergo epoxidation with the oxygen coordinated to a heme group. I would like to bring the ligand closer to the oxygen (via steer) to react. It forms an oxygen (on the heme) to carbon (on the ligand) transition bond.
At the moment, I am defining my rxn coordinate as the distance between the carbon on the ligand and the oxygen of the heme and decreasing that distance over time. The distance between the carbon and oxygen initially is about 3.4 angstroms. Is this the correct way of doing this? Or should I define the ligand as a whole moving towards the oxygen? I wasn't sure if pulling from one atom would "distort" the molecule and greatly increase the work or if that didn't matter here. Thanks!
-Peter Ramdhan
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Received on Sat Jan 11 2025 - 15:00:02 PST
