We recommend igb=8, with mbondi3 radii set in leap, and the ff14SBonlysc
force field. See this article for examples of protein dynamics vs nmr and
protein folding.
Folding Simulations for Proteins with Diverse Topologies Are Accessible in
Days with a Physics-Based Force Field and Implicit Solvent
Nguyen, H., Maier, J., Huang, H., Perrone, V., Simmerling, C., Journal of
the American Chemical Society, 2014, 136 (40), 13959-13962
DOI: 10.1021/ja503277669
PMCID: PMC4195377
On Fri, Dec 27, 2019, 6:54 AM SHAUNAK BADANI <
shaunak.badani.research.iiit.ac.in> wrote:
> Hi,
>
> We have a system containing a protein, and we would like to know what are
> the implicit solvent parameters to be used when conducting molecular
> dynamic runs on it.
> We are curently using the `igb = 1` option, which gives us Hawkins,
> Cramer, Truhlar generalized born models as per the Amber18 manual.
>
>
>
> Regards,
> Shaunak Badani,
> 3rd Year Undergraduate Student,
> International Institute of Information Technology.
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Dec 27 2019 - 06:00:04 PST
