It's built into Amber, but if you want to see all of the details on the
function and parameters they are included in the paper on the model that I
sent earlier.
On Sun, Jan 28, 2018 at 4:09 PM, Siddhartha Jain <tmfs10.gmail.com> wrote:
> In particular if you could point me to where I might obtain the GBneck2
> parameter file, that would be be really helpful.
>
> On Sun, Jan 28, 2018 at 2:22 PM, Siddhartha Jain <tmfs10.gmail.com> wrote:
>
> > I wanted to know where the files that have the parameter sets are as I
> > need to compute the Hessian of the MM-GBSA energy function. But it seems
> > there might be a way to get the Hessian via the mme2 function in NAB? I'm
> > not sure how to go about it however so if you have pointers on how to
> call
> > that function in python, that would be really good.
> >
> > Thanks!
> > --Sid
> >
> > On Sun, Jan 28, 2018 at 9:59 AM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> Can you be more specific about what you mean by GBSA parameters? Amber
> has
> >> several GB parameter sets, with the most recent being the igb=8 model
> >> ("GBneck2"). You can read more about it's development here:
> >> Improved Generalized Born Solvent Model Parameters for Protein
> Simulations
> >> Nguyen, H., Roe, D. R., Simmerling, C., Journal of Chemical Theory and
> >> Computation, 2013, 9 (4), 2020-2034
> >> DOI: 10.1021/ct3010485
> >> PMCID: PMC4361090
> >>
> >> and testing with ff14SB here:
> >> 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
> >>
> >> ff14SB does not have a dielectric constant, that would be a property of
> a
> >> specific material that you simulate rather than the force field itself.
> >>
> >>
> >> On Sat, Jan 27, 2018 at 8:11 PM, Siddhartha Jain <tmfs10.gmail.com>
> >> wrote:
> >>
> >> > Hi,
> >> >
> >> > Where can I obtain the GBSA parameters for the different atom types
> (I'm
> >> > using the ff14SB force field but fine with using others if there
> isn't a
> >> > set of GBSA parameters for the atom types in that FF).
> >> >
> >> > Also what's the dielectric constant for ff14SB?
> >> >
> >> > Thanks
> >> > --Sid
> >> >
> >> > --
> >> > https://tmfs10.github.io
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > https://tmfs10.github.io
> >
>
>
>
> --
> https://tmfs10.github.io
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Received on Sun Jan 28 2018 - 13:30:02 PST
