No you're confusing this with my former part time gig as a male model.
Good times, good times...
On Nov 17, 2011 2:39 PM, "Ken Merz" <merz.qtp.ufl.edu> wrote:
> Scott,
>
> That's how you had so much money while at PSU! Moonlighting!
>
> Kennie
>
>
> On Nov 17, 2011, at 5:19 PM, Scott Le Grand wrote:
>
> > Hey David, 1 ns of sampling barely begins to cover evaluating the
> accuracy
> > of this approximation. In contrast, in my 1993 JCC paper, I randomly
> > generated tens of thousands of uncorrelated conformations, then
> calculated
> > their SASA with my algorithm, an *exact* but expensive algorithm out of
> > Berkeley, and the Still approximation. Just like similar approaches like
> > Kazunori Toma's Residues in a Sphere potential look right for native
> > conformations, once you drift away from the native state, both of these
> > approximations lose meaning. In the MolSurf case you see an overall
> > correlation coefficient of ~0.3 which is essentially random (mine was
> 0.98
> > or so). In fact, Clark Still himself offered me $14K to come up with
> > derivatives for my method in order to replace his. I did so, but I'm not
> > satisfied with their accuracy so I never published or took the money.
> >
> > So the question you have to ask yourself here is: do you feel lucky? Are
> > you comfortable with using a potential term that is chomping at the bit
> to
> > pull you away from the native state into the bizarro universe? I'd post
> > the incriminating diagram but I'm at SC11 right now with no access to
> said
> > paper. It's probably in your library though. Heck, you can probably
> > download it.
> >
> > Scott
> >
> > On Thu, Nov 17, 2011 at 10:26 AM, David A Case <case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Tue, Oct 04, 2011, Scott Le Grand wrote:
> >>
> >>> As someone who wrote a *really* fast SASA approximation 18 years ago
> >>> (basically Shrake and Rupley on steroids), here's my two cents.
> >>>
> >>> The Still et al. approximation at the heart of GBSA has a correlation
> >>> coefficient of ~0.3 with the actual SASA. On the bright side, this
> >>> approximation has a derivative.
> >>>
> >>> So if you're happy with some indeterminate analytic function of the
> >> number
> >>> of atoms surrounding a given atom as a surrogate for accurately
> >> calculating
> >>> the SASA, carry on... I'm not.
> >>>
> >>
> >> I'm moving this from the amber list to the amber-developers list. What
> >> Scott
> >> said didn't agree with what I remembered from a decade ago, so I asked
> Dan
> >> to look into this question, and his initial results are attached.
> >>
> >> Basically, although there are some real limitations with LCPO, a
> >> description of it as an "indterminate analytic function" with low
> >> correlation to the actual SASA isn't correct for this particular test.
> >> Correlation coefficients of 0.86 and 0.99 are found in the two cases
> >> looked at
> >> here.
> >>
> >> So: finding out more about what types of tests lead to the bad results
> >> would
> >> be useful, and it would also be nice to know about other approximations
> >> that
> >> we should consider.
> >>
> >> ....dac
> >>
> >>
> > _______________________________________________
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> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> Professor Kenneth M. Merz, Jr.
> University of Florida Research Foundation Professor
> Edmund H. Prominski Professor of Chemistry
> Department of Chemistry
> Quantum Theory Project
> 2328 New Physics Building
> PO Box 118435
> University of Florida
> Gainesville, Florida 32611-8435
>
> e-mail: merz.qtp.ufl.edu
> http://www.qtp.ufl.edu/~merz
>
> Phone: 352-392-6973
> FAX: 352-392-8722
> Cell: 814-360-0376
>
> "The fundamental laws necessary for the mathematical treatment of a large
> part of physics and the whole of chemistry are thus completely known, and
> the difficulty lies only in the fact that application of these laws leads
> to equations that are too complex to be solved."
>
> PAM Dirac, 1929
>
>
>
>
>
>
>
>
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Received on Thu Nov 17 2011 - 19:00:02 PST
