I see I wasn't specific enough. :-)
On Nov 18, 2011, at 10:28 AM, Scott Le Grand wrote:
> [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 - 11:00:02 PST
