Thank you so much Kellon for the clear instruction. Now my doubt is clear.
My thanks to prof. Simmerling.
Sincerely,
Sunita
On Sun, May 24, 2020 at 11:23 AM Kellon Belfon <kellonbelfon.gmail.com>
wrote:
> 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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Received on Sun May 24 2020 - 06:30:03 PDT
