Subject: Comments on the "MM3 in TINKER" thread

From: <[email-masked]>
Date: Fri, 06 Jun 97 14:39:08 -0500

Dear CCL List,

     In reply to the two messages shown below, we have run calculations
 on 4,5-dimethylphenanthrene using the TINKER package's version of the
 MM3 force field. We get a 4-12-13-5 torsion angle of 29 degrees at the
 "TINKER" minimum. The "official" MM3 value is 32 degrees (31.9) as per
 Allinger, Li, Yan and Tai, JCC, 7, 868-895 (1990). The crystal structure
 is 31.5 degrees, MM2 gives 34.6, etc.

 We need to make the following points:

   (1) TINKER's MM3 is not exactly the same as "official" MM3. It
       differs primarily in two respects. TINKER does not implement
       the "special" functions for the electronegativity, anomeric
       and Bohlmann corrections. TINKER's conjugated pi-system method
       for scaling the bond and torsion parameters differs from that
       used in either MM2 or MM3. It is closer to the MM2 method; PPP-like
       instead of VESCF, and reparametrized by our group to fit a somewhat
       different set of conj. hydrocarbons and heterocycles than the JCC
       paper above.

   (2) 4,5-Dimethylphenanthrene is a rather extreme case, where the exact
       value of the angle listed above is quite sensitive to a combination
       of methyl vdw and pisystem torsional parameters. For example, we
       used the TINKER MM3 to perform a minimization where the 4-12-13-5
       angle is constrained to the X-ray value of 31.5 degrees. The energy
       of this structure is less than 0.04 kcal/mole higher than the energy
       of the 29 degree unconstrained TINKER MM3 minimum. For the vast
       majority of less crowded conjugated systems, we believe that the
       TINKER MM3 results will be very, very similar to "official" MM3.

   (3) Given the exceptions listed above in (1), we believe that our
       MM3 (or for that matter our MM2, AMBER/OPLS, AMBER-95, CHARMM22,
       and so forth) is essentially EXACT. For a great many molecules,
       we know our implementation is EXACT by direct comparision with
       MM3. We have gone to rather great lengths to try to replicate
       the intentions of the authors of the force fields we have
       included in TINKER. That said, we should stress that TINKER
       should not be used as a replacement for "official" MM3, or any
       other "official" force field. If getting "official" results matters,
       then we suggest that you use an "official" program....

   (4) Christoph Etzlstorfer (1st message below) started this thread by
       reporting that he got a phenanthrene angle of 21 degrees using
       TINKER's MM3. We are at a loss to explain his result, and will
       correspond with him separately.

   (5) Stephen Andruski (2nd note below) has gotten a value of 31.6 for
       the dimethylphenanthrene angle using Alchemy 2000. To my knowledge,
       this should be an "official" MM3 calculation since TRIPOS licences
       MM3 from Prof. Allinger. The difference between 31.9 in the JCC
       paper and Andruski's 31.6 might be due to some small change in the
       "official" MM3 parameters (?).

 Anyone who would like to try the TINKER molecular mechanics/dynamics package,
 despite these recent messages to the list, can get the current version 3.3
 with full source code from the Ponder lab web site at:

                     http://dasher.wustl.edu/tinker/

 A new version 3.4 with many new features, increased speed for some types
 of calculations and (yes...) some bug fixes will be available from the
 same site later this month.

                                  Jay Ponder

 ................................................

> The original posting from Christoph Etzlstorfer:
>
> Rencently I downloaded the modeling package TINKER which contains MM3. When
> calculating the structure of 4,5-dimethylphenantrene I found a torsion
> angle 4-12-13-5 (the angle on the ringsystem between the methylgroups) of
> 20.8 degree. In the paper in which MM3 on conjugated hydrocarbons is
> presented (J. Comp. Chem. 11, p. 868 (1990)) it is 31.9 degree with MM3 and
> 31.5 degree with X-ray. The structure in the inputfile had a torsion angle
> of about 35 degree.
>
> Does anyone have any experiences with MM3 in TINKER?
>
> ###################################################################
> Dr. Christoph Etzlstorfer       Phone:  *43-732-2468-750
> University of Linz              Fax:    *43-732-2468-747
> A-4040 Linz               E-mail: [email-masked]
> Austria                   http://ocwww.chemie.uni-linz.ac.at
> ###################################################################

 ..................................................

> The original posting from Stephen Andruski:
>
>     I do not have any experience with MM3 in TINKER, but I ran a quick 
>     calculation with Alchemy 2000 which also has an implementation of MM3. 
>      The angle in question minimized to -31.6 degrees which is in very 
>     good agreement with the X-ray structure and the previously published 
>     MM3 value.
>     
>     Something in TINKER's implementation must be off.
>     
>     Dr. Stephen W. Andruski
>     FMC Corporation
>     [email-masked]

--------
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/