Changes to intrinsic Born radii can be made using parmed.
You may want to rwad our more recent protein gb model paper to see further
discussion and a table of radii.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361090/
On Sat, May 23, 2020, 9:54 AM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> Dear Amber-users,
>
> I want to perform a REMD simulation with GB-OBC implicit solvent model. In
> the following papers it is mentioned that saltbridges are overstabilized in
> GB-OBC model. I want to reduce the GB radius for hydrogen atoms involved in
> saltbridges to 1.1 Ang as mentioned in the following papers. I am not clear
> where exactly I need to make the changes to satisfy the criteria.
>
> Your help will be highly appreciated.
>
> 1) Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling,
> C. Investigation of Salt Bridge Stability in a Generalized Born Solvent
> Model. J. Chem. Theory Comput. 2006, 2, 115−127.
>
> 2) Shang, Y.; Nguyen, H.; Wickstrom, L.; Okur, A.; Simmerling,
> C. Improving the Description of Salt Bridge Strength and Geometry
> in a Generalized Born Model. J. Mol. Graphics Modell. 2011, 29, 676−
> 684.
>
> Sincerely,
> Sunita
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Received on Sat May 23 2020 - 07:30:02 PDT
