Dear Dr. Case
Thanks for your reply.
Your reply gets me to ask for a reference (including a methodology) for GB radii parameterization in amber force field.
Thanks so much
Eliac
--- On Thu, 1/20/11, case <case.biomaps.rutgers.edu> wrote:
> From: case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Story of bugfix 18-Amber10
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Thursday, January 20, 2011, 3:43 AM
> On Wed, Jan 19, 2011, Eliac Brown
> wrote:
>
> > I was wondering what is the story of bugfix 18 in
> amber10.
> > I put an extra point on my ligand for better hydrogen
> bond description
> > with the active site, and calculated the GBSA energy
> without any
> > problem.
> > So, why you implemented bugfix 18 which asks for no GB
> with extra-pint?
>
> The amber GB force fields have never been parameterized
> with extra-point
> protein or nucleic acid potentials. Under most
> circumstances, try to combine
> those two would be a mistake. In particular, there
> are no default dielectric
> radii to use for extra points.
>
> If you understand the code well enough to add your own
> extra points, and to be
> sure that you are not seeing any problem, then it is easy
> enough for you to
> disable the check that bugfix 18 introduced.
>
> ...dac
>
>
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Received on Wed Jan 19 2011 - 23:30:05 PST
