Re: [AMBER-Developers] Accuracy of the LCPO approximation

From: Scott Le Grand <varelse2005.gmail.com>
Date: Fri, 18 Nov 2011 10:28:27 -0800

[image: image.jpeg]

Happy?

On Fri, Nov 18, 2011 at 8:40 AM, Eric Pettersen <pett.cgl.ucsf.edu> wrote:

> If you're going to have this discussion on list, at least have the decency
> to attach photos.
>
> --Eric
>
> On Nov 18, 2011, at 3:54 AM, Ken Merz wrote:
>
> > Oh, I forgot about that stripping gig on mountaintop. K
> >
> > On Nov 17, 2011, at 9:53 PM, Scott Le Grand wrote:
> >
> >> 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
> >>>>>
> >>>>>
> >>>> _______________________________________________
> >>>> AMBER-Developers mailing list
> >>>> 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
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER-Developers mailing list
> >>> AMBER-Developers.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> 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
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>





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Received on Fri Nov 18 2011 - 10:30:07 PST
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