Thanks Robert, I figured it must be available somehow - almost everything
is :) I would mention thought that "show minimization" isn't in the docs
as far as I see at
http://chemapps.stolaf.edu/jmol/docs/?&fullmanual=1&ver=14.2#show. Good
thing to add, unless I just missed it!
That leaves me with 2 questions:
1) Is the easiest thing to do to get this data into arrays just to parse
the output of "show minimization", or are these already stored in some more
convenient format?
2) This might be just my admittedly inaccurate assumption, at least in some
cases, that molecular mechanics models have an intuitive "real world"
representation (meaning, e.g., the stretch term truly equates to stretch,
and the bend term truly equates to bend, etc.), but the mmff94 results (and
I've seen this with mm+ in HyperChem also) don't seem to break down as I
would think. For example, cyclopropane has a lot of ring strain (estimated
at 27.6 kcal/mol in the literature), the majority of which comes from angle
strain, not torsional strain (~9 kcal/mol).
mm+ VASTLY underestimates both total strain and angle strain. mmff94
substantially overestimates torsional strain while again vastly
underestimating angle strain (mmff94 actually overestimates total strain,
storing a lot of it in an "electrostatic" category. Note that the lack of
agnel bending strain energy seems to come from the fact that both of the
force fields seem to be using a reference angle of 60 degrees for
tetrahedral carbon, which is actually ideally 109.5 degrees. I know in the
case of mm+ this is on purpose -- 3 and 4 membered carbon rings get
assigned special reference values, so I assume the same thing is happening
in mmff94.
Which brings me to the question: Do these energy numbers, and the breakdown
of the energies into the various categories, really mean anything? Or
should I just think of them as being abstract equations that are used to
curve fit the molecular mechanics energy minimization to empirical data?
Or, do they actually work fairly well in most cases and I've just picked
some weird edge cases where the parallelism of the formulas and the real
world break down?
I know #2 isn't really a Jmol topic, but rather computational chemistry in
general. If you'd prefer, and anyone is interested in discussing this off
list, I'd really like to talk to someone who has more experience with this
than I.
Sincerely,
James Ryley, PhD, Patent Agent
SumoBrain: Intellectual Property Solutions & Data
AcclaimIP <https://www.acclaimip.com/> |
FreePatentsOnline.com<http://www.freepatentsonline.com/>|
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This communication is confidential and may be subject to legal privilege.
Nothing contained herein should be construed as legal or patenting advice.
On Sat, Feb 22, 2014 at 3:15 PM, Robert Hanson <[email protected]> wrote:
> Yes, James, there is. It is no so much "bond" data, but structural data
> involving from 2 to 4 atoms. To get this, simply use:
>
>
> *minimize energy*
>
> *show minimization *
> To understand the tables, I would direct you to MMFF MMFF94 Force Field --
> T. A. Halgren, J. Comp. Chem. 5 & 6 490-519ff (1996).
>
> Bob
>
>
>
> On Sat, Feb 22, 2014 at 10:32 AM, James <[email protected]> wrote:
>
>> Hi,
>>
>> If you minimize a structure, you end up with an energy, which is
>> presumably the sum of all the bonds' variations from ideal lengths and
>> angles (including torsion), plus any non-bonded forces involved (e.g., Van
>> der Waals -- although I would think these end up being represented as
>> changes in bonding also, since these forces must affect the bonds as they
>> push/pull on things). Most programs, including Jmol, output this energy as
>> a single total number for the molecule. But, it seems that the program
>> must, in order to sum the energies, how each individual bond varies from
>> what the force field would consider a 0 energy configuration.
>>
>> Is there a way to get at this data? For example, to list each bond, its
>> reference angle and length, its actual angle and length (I know this can be
>> accessed), and how much it contributes to the overall single point energy?
>> Reference heat of formation would be nice too, if available, since that
>> would let you calculate a percent change in bond energy rather than just
>> the difference from 0, although it certainly isn't clear to me that the
>> system even possesses that information.
>>
>> Sincerely,
>> James Ryley, PhD, Patent Agent
>> SumoBrain: Intellectual Property Solutions & Data
>> AcclaimIP <https://www.acclaimip.com/> |
>> FreePatentsOnline.com<http://www.freepatentsonline.com/>|
>> SumoBrain.com <http://www.sumobrain.com/> |
>> BioMedSearch.com<http://www.biomedsearch.com/>
>>
>> This communication is confidential and may be subject to legal privilege.
>> Nothing contained herein should be construed as legal or patenting
>> advice.
>>
>>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
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