OK, SMARTS-based MMFF94 charges are now checked in for Jmol.
Obviously the settings are not perfect and will take some tweaking. I'm
sure it's more complicate than I make it out to be -- probably some very
odd definitions in there; certainly some I could not fathom on this first
pass. I haven't taken a full look at OpenBabel's definitions, but I did use
the algorithm in OBForceFieldMMFF94::SetPartialCharges() as my basis (even
though some of that makes almost no sense to me -- for example:
switch (type1) {
case 32:
// 32 OXYGEN IN CARBOXYLATE ANION
// 32 NITRATE ANION OXYGEN
// 32 SINGLE TERMINAL OXYGEN ON TETRACOORD SULFUR
// 32 TERMINAL O-S IN SULFONES AND SULFONAMIDES
// 32 TERMINAL O IN SULFONATES
case 35:
// 35 OXIDE OXYGEN ON SP2 CARBON, NEGATIVELY CHARGED
case 72:
// 72 TERMINAL SULFUR BONDED TO PHOSPHORUS
factor = 0.5f;
break;
case 62:
// 62 DEPROTONATED SULFONAMIDE N-; FORMAL CHARGE=-1
case 76:
// 76 NEGATIVELY CHARGED N IN, E.G, TRI- OR TETRAZOLE ANION
factor = 0.25f;
break;
}
What the heck is that? Convince me that is reasonable! (Or are these not
the MMFF94type numbers in MMFF-I_AppendixB.ascii?)
Jmol's aromatic definition is structural, not electronic, so that certainly
would be one point of difference.
Ideally it would be verified, but for a lot of purposes at least for now
I'll be satisfied with an approximation.
I can get partial charges from MMFF94 far easier from PubChem than I can
from OpenBabel, I think. All I have to do is
load :xxxxx
then save the partial charges in an array and compare them with calculated
values:
load :methanol
A = {*}.partialcharge.all
calculate partialCharge
{*}.partialcharge = A.sub({*}.partialcharge.all)
label %[partialcharge]
print {*}.partialcharge.all.stddev
This will display the differences and print the standard deviation. I must
be doing something right, because I do get this:
$ load :methanol
...
0.0
$ load :acetone
...
8.1649824E-4
$ load ":ethyl acetate"
...
3.9223014E-4
$ load ":benzene"
...
0.0
$ load :pyridine
...
0.0
But I'm sure there are plenty that are problematic.
Caffeine must assign different atom types --
load :caffeine
A = {*}.partialcharge.all
calculate partialCharge
{*}.partialcharge = A.sub({*}.partialcharge.all)
label %[partialcharge]
print {*}.partialcharge.all.stddev
0.10437195
But that's what I expect at this stage. Can't expect everything to be
perfect in a day!
Can I get OpenBabel to report what MMFF94 atom types it is assigning?
Bob
On Fri, Apr 27, 2012 at 8:00 PM, Geoffrey Hutchison <geo...@pitt.edu> wrote:
>
>
> > Geoff, I will look at that. What does "fully validated" mean exactly?
>
> There's an MMFF94 validation set:
> http://ccl.net/cca/data/MMFF94/
>
> This includes 761 structures, plus energies, etc. But one reason I bring
> this up, is that you can use Babel to generate partial charges (e.g., for
> mol2 files):
> echo "c(s1)ccc1Cl" | babel -ismi --gen3d --partialcharge mmff94 -omol2
>
> In short, feel free to use Babel to generate a pile of MMFF94 charges for
> testing. IIRC, the structures in the test set also have MMFF94 charges.
>
> > I have the SMARTS business for MMFF94 charges working in Jmol now for
> getting the atom types -- obviously not validated! -- and I suspect it will
> require a bit of hand-crafting.
>
> We'd be interested in testing SMARTS versus the hand-crafted rules in Open
> Babel.
>
> Hope that helps,
> -Geoff
>
>
--
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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