[AMBER] 回复: Specifying Restraints Question

From: Huang ZiJian via AMBER <amber.ambermd.org>
Date: Fri, 29 Dec 2023 11:35:48 +0000

Hi,

"ibelly" is what u need.

Regards,
Zijian

________________________________
发件人: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
发送时间: 2023年12月29日 16:17
收件人: AMBER Mailing List <amber.ambermd.org>
主题: [AMBER] Specifying Restraints Question

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 - 04:00:02 PST