[AMBER] MCPB, how to treat protein-attached Ru-dye

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Thu, 30 Dec 2021 12:48:49 -0500

Dear Amber Community,

I’m wondering how to use MCPB to parameterize Ru(bpy)2(4-BrCH2-4’-CH3-bpy), where the Br is replaced by the S of a Cys sidechain. Specifically, how do I define the parameters for the Cis-dye linkage? I know how to run MCPB for the dye by itself, but it’s the linkage to the protein that befuddles me.


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Received on Thu Dec 30 2021 - 10:00:03 PST
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