Thank you, Nico, for releasing Jmol 12.3.25. This version of Jmol is very
special. It includes
set forcefield "MMFF"
which does just what you think it does -- uses MMFF94 for the forcefield
for the MINIMIZE command. Note that MINMIIZE ENERGY will just take a single
point, with no position changes, and MINIMIZE itself will do the
minimization. There are also several other options already described in the
documentation.
set forcefield "UFF"
is the default still. We can discuss whether we want to keep it that way or
whether we want UFF to be a 'backup' for MMFF94 (used when the atoms are
other than just the few the MMFF94 is parameterized for).
Note that the variable _minimizationEnergy holds the results of the energy
calculation in case you want to access that.
As a bonus, we get the MMFF94 calculated partial charges as well. The
command
calculate partialcharge
does NOT depend upon the FORCEFIELD setting, since UFF does not use
electrostatic energy in its calculation. Interestingly, I learned from this
experience that MMFF94 structures are almost *entirely* based on
electrostatics -- the energies there are about 10 times any other
calculated energy. Very interesting to me, because it suggests that
equilibrium structures of actual molecules are almost entirely based on
balance of charge. I hadn't thought about it that way, but it might be
right.
How good is the implementation?
It's pretty good. All MMFF94 atom types and formal charges are validated
(use LABEL %[atomType] to see those) over a 761-compound 17,000-atom
validation set. Charges are good to +/-0.001 charge unit of what MMFF94
specifies, which is basically the precision of the data. Energies are
within 0.1 kcal/mol for 748 of the 761 structures, with most energies
within a few thousandths of a kcal/mol, and that, too, is about the
precision of the parameter data. Thirteen somewhat obscure structures will
not validate (with energy differences from the MMFF94 references of
0.15-1.5 kcal/mol off), and that is because there are some "empirical
rules" that are still unkown to me relating mostly to sulfur and phosphorus
in 5-membered rings, and probably are not really worth implementing anyway.
These structures, if you read the fine print in MMFF94, are reported with
the following warning:
WARNING - Conformational Energies May Not Be Accurate
(Yeah, like that's not true of the entire set!) If someone wants to show me
how to do that, I'm game.
Getting this set up was a grand challenge, and I'm pleased with the
results, and especially happy that it only took a couple of weeks out of my
life. We now have a very efficient algorithm for setting up and evaluating
the various calculations, especially atom typing, charge calculation, angle
and torsion collecting, and van der Waals/electrostatic calculations. It
was a fun challenge to develop Jmol SMARTS searching for these purposes and
to come up with bond-based rather than an atom-based, algorithms for
determining angle, torsion, van der Waals, and electrostatic interactions.
I really enjoyed putting this together. It's going to be hard to beat!
Many thanks to Kyle Lutz -- and a challenge to you, Kyle, to get chemKit to
do even better!
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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