Hi Tejas,
I wrote a tutorial about this exact problem, using the Amber protein
forcefields:
https://robinbetz.com/blog/2016/11/28/parameterizing-an-isopeptide-bond/
Since you have LYS-GLY, you can use the exact frcmod for the additional
bond terms.
Hope this helps,
Robin
On Wed, Mar 15, 2023, 8:50 PM Shah, Tejas V. via AMBER <amber.ambermd.org>
wrote:
> 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 - 21:30:02 PDT
