Hi Sunita,
In the page 4 last line, it is written that no need to modify the Born
radius of HN+ in Lys. Why?
In the paper two radii were adjusted, (1) the oxygen of the negative
charged amino acid and (2) the hydrogen of the positive charged amino acid.
Those adjustments are being done to match the target PMF (salt bridge PMF
in TIP3P).
That line suggested that the adjustment of the oxygen radius was sufficient
to match the target PMF and therefore no adjustment of the hydrogen radius
was needed for the KAAE system. I hope this is helpful or clear.
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?
Yes ensure you use ff14SBonlysc and not ff14SB (source
leaprc.protein.ff14SBonlysc)
And change to the mbondi3 radii to get the radii from the paper.
set default PBRadii mbondi3
On Sat, May 23, 2020, 11:59 PM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> 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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Sat May 23 2020 - 23:00:02 PDT
