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
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
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Received on Sun Jan 28 2018 - 11:30:01 PST
