Dear Amber Community,
How can I specify that all residues beyond some distance from an active site residue should be restrained, while all residues within the distance threshold are free to move?
For example, a studying using AMBER states:
"During the QM/MM free energy simulations, residues with any atom within an 18 Å radius of a sphere centered at the Y731:OH atom were allowed to move, with the remaining atoms kept fixed.” (J. Am. Chem. Soc. 2021, 143, 16, 6054–6059)
Best,
Matthew
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Received on Fri Dec 29 2023 - 00:30:02 PST
