Dear Prof. Simmerling,
Thanks for sending the paper link. Now I am going through it. So basically
GB-Neck2 improves solvation energy and effective radii resulting in better
treatment of saltbridges. We can implement this in our simulation using
igb=8 in AMBER 11 or later. GB-Neck2 simulation uses mbondi3.
In the page 4 last line, it is written that no need to modify the Born
radius of HN+ in Lys. Why?
In the AMBER manual it is mentioned that the ff14SB force field with igb=8
produces the best result for proteins. If I want to use GB-Neck2 for my
REMD simulation then only this modification I need to incorporate. Am I
right?
With sincere regards,
Sunita
On Sat, May 23, 2020 at 7:53 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat May 23 2020 - 21:00:02 PDT
