Subject: Re: CCL:the MM2 (big) family

From: [email-masked] (Per-Ola Norrby)
Date: Thu, 13 Mar 1997 10:14:00 +0100

Dear Alexandre,

        The list of MM2s you gave is a good starting point.  I do have a
few additions.

        First, I think you should list all the cases where Allinger himself
drastically changed the functional form.  The original version is MM2(77),
and  MMP2 came as a separate program in 1980 (I think, I'm not entirely
sure of all dates I'll give below).
        The MM2(85) combined  MM2 and MMP2 into one program, so that is a
functional change.  With this version, MM2 reached a kind of maturity
plateau.  There were later changes, but not any drastic improvements in
overall performance.  There were new versions in 1987 and 1991, and at
least the MM2(87) version included changes in functional form.  There are
many "minor" functions in MM2, like electronegativity effect and anomeric
effect, I cannot say for sure when they were added, but I believe that all
were in MM2(87).  I think MM2(91) was just a parameter update, but I'm not
sure.  In 1994 was published the parameter estimator for MM2 (and MM3), "J.
Mol. Struct (THEOCHEM) 312 (1994) 69-83", but I haven't seen an
implementation for MM2 (it is in MM3[94]).

        Other implementations:

        TINKER, from Jay Ponder (info at http://dasher.wustl.edu/)
                The Chem3D parameters were originally from TINKER

        You lacked a reference for Chem3D, see: http://www.camsci.com/

        CAChe from Tektronix has an "augmented" MM2.

        Spartan from Wavefunction includes an MM2 with the original
        parameter set, but no conjugated calculations!  A bit dangerous,
        but...  See: http://www.wavefun.com/

        In the MacroModel manual I also found references to Osawa, "Tet,
2769 (83)", and Kroon-Batenburg, "JMolStr, 417 (83)", I don't know if both
qualify as separate implementations according to your rules.

        I know that several workers in the inorganic/organometallic field
have extended MM2 to higher coordination.  You could use the review by
Benjamin Hay as a starting point, "Coord. Chem. Rev. 126, 177-236 (1993)".
Many (I'm among them) have also solved special coordinations in MM2 without
changes to the functional form using tricks like dummy atoms and fixed
atoms, I don't know if that qualifies ( MM2 definitely wasn't INTENDED to
be abused so, that's for sure... :-).

        Regards,

        Per-Ola Norrby

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 *  Per-Ola Norrby, Associate Professor
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
 *  Universitetsparken 2, DK 2100 Copenhagen, Denmark
 *  tel. +45-35376777-506, +45-35370850    fax +45-35372209
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---

From: <[email-masked]>
Date: Thu, 13 Mar 97 11:51:17 -0600

Dear Alexandre Hocquet,

      I can tell you something about one "family" of MM2 versions. The code
 distributed as "MM2" in the Chem3D package is actually my code written
 completely from scratch and based on MM2 circa 1987. It is IDENTICAL to
 "real" MM2 in all basic functional forms with the following exceptions:

     (1) It adds a quartic term to the bond stretch (just the next term
         in the Taylor expansion of the Morse potential, "real" MM2
         uses the first two, harmonic and cubic, while we added the
         quartic). This has essentially no effect on minimum energy
         structures and energies (often less than 0.0001 kcal difference),
         but was added to make molecular dynamics stable, exp. at high
         temperature. Allinger's group has added this same term to MM3.

     (2) Our "MM2" uses the identical dipole-dipole term to real "MM2", but
         it also allows (in addition) use of partial charges (needed, for
         example to get the correct formal charge on a carboxylate, etc.).
         Then our code actually does electrostatics as a sum of the
         dipole-dipole, charge-charge and charge-dipole interactions. Again
         this same mechanism was subsequently implemented in MM3.

     (3) Our code uses a "hybrid" method for conjugated systems that is
         somewhat intermediate between the old MMPI and "real" MMP2.
         We use a straight PPP MO method instead of the "variable electroneg"
         style method, and we have calibrated the internal parameters to
         give good results on a number of kinds of heterocycles. The
         overall differences in results from MMP2 are small, but not zero.

     (4) Our code does not implement any of the special "parameter tweaking"
         terms that are in MM3 and in some versions of MM2, things like
         the electronegativity effect, anomeric effect, Bohlmann effect, etc.

 A later version of our MM2 (as well as an MM3 semi-clone) is available in
 the free molecular mechanics/dynamics package TINKER, which can be obtained
 with source code from http://dasher.wustl.edu/tinker. We have added many,
 many other options, parameter sets, etc., but it is possible to get TINKER
 to give a pretty authentic rendition of MM2 by turning off the bells and
 whistles.

                     Hope this helps, Jay Ponder

--------
Jay W. Ponder				Phone:	(314) 362-4195
Biochemistry, Box 8231         		Fax:	(314) 362-7183
Washington University Medical School
660 South Euclid Avenue			Email:	[email-masked]
St. Louis, Missouri 63110  USA		WWW:	http://dasher.wustl.edu/