Here's my final result. I'm satisfied; I'm pretty sure there is no way to
reproduce the results of the OPTIMOL results exactly. In the cases below
I'm convinced there are bugs in OPTIMOL -- mostly in not consistently
recognizing 5-membered rings, but also there is something odd going on in
the empirical bond parameter calculation.
Bob
# version=12.3.26_dev
#
# code: adding empirical rules to MMFF94 calculation
#
# checkmm.spt;checkAllEnergies
#
# checking calculated energies for 761 models
# 1 COMKAQ E= -7.3250003 Eref= -7.6177 diff= 0.2926998
# 2 DUVHUX10 E= 64.759995 Eref= 64.082855 diff= 0.6771393
# 3 FORJIF E= 35.978 Eref= 35.833878 diff= 0.14412308
# 4 JADLIJ E= 25.104 Eref= 24.7038 diff= 0.4001999
# 5 PHOSLA10 E= 111.232994 Eref= 112.07078 diff= 0.8377838
# 6 PHOSLB10 E= -93.479004 Eref= -92.64081 diff= 0.8381958
#
# for 761 models, 6 have energy differences outside the range -0.1 to 0.1
# with a standard deviation of 0.05309403
#
# a comment about empirical bond parameter calculation:
#
# // Well, guess what? As far as I can tell, in Eqn 18 on page 625,
# // the reduction term and delta are zero.
#
# // -- at least in the program run that is at the validation site:
# // OPTIMOL: Molecular and Macromolecular Optimization Package
17-Nov-98 16:01:23
# // SGI double-precision version ... Updated 5/6/98
# //
# // This calculation is run only for the following three structures. In
each case the
# // reported validation values and values from Jmol 12.3.26_dev are
shown. Clearly
# // the r0 calculated and final energies are very good. subtracting off
0.008 from
# // r0 would certainly not give the reported values. Something is odd
there.
# //
# // bond red* r0(here/valid) kb(here/valid)
Etotal(here/valid)
# //
---------------------------------------------------------------------------------------
# // OHWM1 H1-O1 0.03 0.978/0.978 7.510/7.51
-21.727/-21.72690
# // ERULE_03 Si1-P1 0.0 2.223/2.224 1.614/1.609
-2.983/ -2.93518
# // ERULE_06 N1-F1 0.0 1.381/1.379 5.372/5.438
1.582/ 1.58172
# //
# // *reduction and delta terms not used in Jmol's calculation
#
#
--
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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