[AMBER] AMBER Parameters for LYS-GLY Isopeptide bond

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From: Shah, Tejas V. via AMBER <amber.ambermd.org>
Date: Thu, 16 Mar 2023 03:50:17 +0000

Hello Everyone,

For one of my projects, I want an LYS-GLY isopeptide bond in my system. I am currently trying to develop the FF parameters using the PyRED server. Could anyone please advise on how to approach this?

I tried two approaches as described by Venkat (http://archive.ambermd.org/202111/0115.html)

  1. I have tried to run the entire molecule N-glycidyl-lysine, but when I substitute the residue name in my PDB it adds the entire residue whereas I want it to split between two chains.

  1. If I parametrize them separately, then I fear it may not generate the bond, angle, and torsion parameters for isopeptide bond.

  1. Do we have parameters available?

Thank you.

-Tejas.
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Received on Wed Mar 15 2023 - 21:00:02 PDT