Subject: the MM2 family summary

From: Alexandre Hocquet <[email-masked]>
Date: Wed, 26 Mar 1997 01:33:54 +0000

Estimados CCLers,
here is a summary of answers to my MM2 census. Thank you to all that
answered, especially Jay Ponder and Per Ola Norrby.
The original question is quoted first.

--------------------------
I am currently attempting to make a census of the MM2 versions,
those natural sons that are based upon, but not identical
 to (they are no clones) one of the official Allinger's MM2 
versions.

Of course they are thousands if one counts as a new version a MM2 to
which were added a few parameters.

For the purposes of my inventory, i will define a *different* version,
one that differs in :
- the equations of the force field terms (stretch, Van der Waals...)
- the definitions of the nonbonded terms (point charges for bonds
dipoles)
- the treatment of conjugation
- evaluating parameters that are not defined
- recognizing substructures
- treatment of strucures with more than 4 bonds attached to an atom

Taking (Gundertofte et al., J.Comput.Chem., 1996, p429) as a starting
point,
i can name :

MM2*(Macromodel) : Mohamadi et al., J.Comput.Chem., 1990, p440

"MM2" (Chem3D) : no reference

MMX (PC model) : Gajewski et al., Advances in Molecular Modeling, Liotta
Ed, JAI Press, Greenwich, CT, 1990
**If someone has a reprint of this reference, i am highly interested**

an MMP2 variant : Liljefors et al., J.Comput.Chem., 1985, p478

Furthermore i can quote :

MM+ (Hyperchem) : no reference

MM2X (Optimol) : Holloway et al., J.Med.Chem., 1995, p305

If you know others, please let me know. Also, if you know other criteria
that could be pertinent to define a *different* version, do not hesitate
either.
----------------------------
Dear Alexandre,

I have completed this task by analysing and comparing of the original
MM2, MMX within the PCMODEL, MM2 within Spartan and MM2 within the OFF
of the Cerius2 by MSI. The work will be published soon. 
The main conclusion was that each implementation has something special
what the others does not have (conjugation, treatment of vdW
interactions, source of the atomic point charges and/or bond dipole
moments or increments). 
Therefore, if you want to move from one software to another you should
take care for the parameters.
Well, it will be a really hard work - I know - and let me know if you
need any help or you want to have the results of the Open Force Field
within Cerius2 or the Spartan.
Furthermore, if you are not aware from working together via
electronically I am happy to join to you!
-- 
    
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        Robert K. Szilagyi                  Mueller Laboratory
          ph.d. student                     Dept. Organic Chemistry
                                            University of Veszprem
       [email-masked]                 Veszprem, H-8201
                                            POB. 158; Egyetem u. 10.
     Phone:  +36 88 422022 extn. 395        HUNGARY
     Mobile: +36 20 461413
     Fax:    +36 88 427492                  http://mm1.vein.hu/

=====================================================================
Para aniadir a tu lista:

MM2 (Molgen)

Molgen es un programa de modelizacion molecular
que funciona bajo MS-DOS. Entre sus capacidades
se cuenta la minimizacion con el campo de fuerzas
MM2. Hasta hace poco era distribuido en los USA
por Eric Slone, pero recientemente ha pasado a
ser de dominio publico y puede obtenerse en los
archivos del CCL:

http:/www.ccl.net/ccl/software.html

Un saludo.

Jose I. Garcia

        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
 *  Internet: [email-masked], http://compchem.dfh.dk/

 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/

Dear Alexandre Hocquet,
        I do not know whether this belongs to the list you plan to make.
I have
one version of the MM2 program with conformational search procedure,
MC-MM2, Tetrahedron, 51, 6789 (1995). The force field (equations and
constants) is inchanged original MM2(87). The DRIVER subroutine is
supplemented by Monte Carlo type routine to enable searching of the
conformational space by random variation of randomly selected torsional
angles. Besides I think that Osawa published MM2' in Tetrahedron with
some
new parameters.
        Best regards.
        Sincerely,
            Ljiljana Dosen-Micovic, e-mail: [email-masked]
            Faculty of Chemistry
        University of Belgrade
        Belgrade, Yugoslavia

-- 
Alexandre Hocquet

Laboratorio de Cristalografía
Facultad de Ciencias Físicas
Universidad de Chile
Blanco Encalada, 2008
Santiago Centro
Chile
fono : 56 2 678 45 19
fax : 56 2 696 73 59
email : [email-masked]