On Mon, Feb 03, 2025, Tej Tarun Sharma 2310225 via AMBER wrote:
>
>I would like to understand the role of the protein scaling parameters (*Sh*,
>*Sc*, *Sn*) provided for igb=8 in Section 4.1 of the Amber manual.
>Specifically, how are these parameters incorporated into the force field
>expression?
You don't indicate whether or not you have studied references [28] and [216]
in the Amber24 Reference Manual, where the igb=8 model is described. The
scaling parameter date back to early work by Hawkins and Truhlar. Among may
other places, you could look at Eq. 14 in Annu Rev Biophys 48:275-296
(2019).
...hope this helps....dac
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Received on Mon Feb 03 2025 - 10:30:03 PST
