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
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 27 2011 - 10:00:03 PDT
