It's not clear what "standard" means here. A specific reference or input
flag is needed to know which you mean.
I suggest as a start to compare your protocol to these recent amber studies
of protein and peptide folding :
Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit
Solvent Simulations of Proteins on CPUs and GPUs
Huang, He and Simmerling, Carlos Journal of Chemical Theory and
Computation, 2018,
DOI: 10.1021/acs.jctc.8b00413
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 Mon, Nov 5, 2018, 11:50 PM Mijiddorj B <b.mijiddorj.gmail.com wrote:
> Dear Hai,
>
> Thank you very much for your prompt reply. I used the "standard" pairwise
> generalized Born model using the default radii with amber.ff14SB.
>
> Best regards,
> Mijiddorj
>
> On Tue, Nov 6, 2018 at 1:17 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > Which GB model + force field you're using?
> > Just make sure your simulation is converged (e.g: starting from two
> initial
> > structures and getting similar popular between 2 simulations).
> >
> > In general, it's hard to do the right thing random coil structure since
> > lots of GB models tend to favor more compacted topology.
> >
> > Hai
> >
> > On Mon, Nov 5, 2018 at 10:18 PM Mijiddorj B <b.mijiddorj.gmail.com>
> wrote:
> >
> > > Dear Amber Users,
> > >
> > > I would like to discuss about the effects of implicit solvents for the
> > > folding simulation. I used the implicit Generalised Born solvent for
> the
> > > linear structure of amphipilic peptides based on the sequence. I
> > simulated
> > > 100 ns, and I was formed alpha helical structure. Experimentally, it
> > shows
> > > random coil structure in the water.
> > >
> > > What do you think? please advice me.
> > >
> > >
> > > Best regards,
> > > Mijiddorj
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> > >
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Received on Tue Nov 06 2018 - 04:00:02 PST
