Our igb8 paper is finally published.
http://pubs.acs.org/doi/abs/10.1021/ct3010485
On Wed, Apr 27, 2011 at 1:48 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Just to add to the good comments of Jason since our manuscript on the GB
> model development is not yet out:
>
> GB models and radii sets are somewhat independent.
> the igb=8 model was actually fit to PB data where both solvent models
> used mbondi2 radii, so in principle it will work well with mbondi2. After
> fitting the model to PB, we made a few additional tweaks to the radii in
> order to improve agreement with explicit solvent data. It is definitely
> better to use mbondi3, but if that is not practical our data shows that it
> is still better to use igb=8 with mbondi2 than other GB models in amber.
> carlos
> On Wed, Apr 27, 2011 at 12:57 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hello,
> >
> > On Wed, Apr 27, 2011 at 7:48 AM, Oliver Kuhn <oak.amber.googlemail.com
> > >wrote:
> >
> > > Hi Jason,
> > > I have read about the igb=8 option.
> > > My version of MMPBSA.py tells me that igb=8 is not available.
> > > Will it run with AmberTools 1.5?
> > >
> >
> > What Bill said is correct -- this is an orthogonal statement. igb = 8
> > currently requires a *different* radius set than what's provided in leap.
> > So-called "mbondi3" radius set. It's the mbondi2 radii with
> modifications
> > the carboxylate oxygen radii (in the deprotonated state), and
> modifications
> > to ARG hydrogens.
> >
> > There is currently no utility available for setting this radius set in
> the
> > Amber distribution, so unless you read the original paper from the
> > Simmerling group and assign the radii by hand in the topology file,
> there's
> > no way of *properly* using it right now.
> >
> > I'm working on a Python script (I do love python...) right now that will
> > allow you to change the radii set to any set you want (including the one
> > needed for igb = 8), but I'm working out some of the kinks for Nucleic
> > acids
> > now. We may try to release it afterwards as some sort of supplement to
> AT
> > 1.5
> >
> >
> > > Another question:
> > > What do you think about the usage of internal dielectrics 2 and 4 in
> > > MMPB/GBSA calcuations?
> > > I get results closest to experimental value when using 1.* *But I would
> > > also
> > > like to know if there is a profound reason to use 1, I mean, is
> something
> > > in
> > > the procedure parameterized to 1?
> > >
> >
> > GB should probably use 1, since that was used in the parameterization.
> > Note
> > that the internal dielectrics have different meanings in GB and PB. In
> PB,
> > it's reasonable to use dielectric constants of 2 or 4 to account for
> > electron polarizability (account for electronic degrees of freedom in a
> > mean
> > field way). When I say reasonable, I mean it's been done before and is
> > supported (and probably attacked) in the literature.
> >
> > The "internal dielectric" for GB, on the other hand, is supposed to be
> the
> > dielectric for vacuum. What GB actually calculates is the delta G of
> > solvation in moving from one environment (vacuum) to another (water).
> The
> > internal dielectric constant of the protein itself actually cancels in
> the
> > derivation of the GB equations. Therefore, changing the internal
> > dielectric
> > constant in GB is akin to changing what you're calculating --> instead of
> > looking at the delta G of transferring the molecule from vacuum to water,
> > you're transferring it from an organic liquid (of dielectric constant 2
> or
> > 4
> > or whatever you set) into water.
> >
> > Of course, the method is so parametrized that it's probably hard to take
> > much physical meaning out of the dielectric constants. Long story short
> --
> > you should probably leave the GB dielectric constants alone since it's so
> > heavily parametrized for water (which is why we removed those as input
> > variables in MMPBSA.py), but it's more reasonable to change dielectric
> > constants in PB calculations.
> >
> > HTH,
> > Jason
> >
> >
> > >
> > > Greets,
> > > Oliver
> > >
> > > --
> > > Oliver Kuhn, Department of Bioinformatics,
> > > Center for Medical Biotechnology, University of Duisburg-Essen,
> > > Universitätsstr. 1-5, 45141 Essen, Germany
> > > phone +49 201 183-3121, oliver.kuhn.uni-due.de
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Mar 07 2013 - 11:30:03 PST
