Subject: Validation suite for MMFF94s (see J. Comp. Chem., May 1999 issue)

From: "Halgren, Thomas" <[email-masked]>
Date: Mon, 26 Apr 1999 19:42:16 -0400

Dear CCLers,

Jan Labanowski has kindly posted on the Computational Chemistry List
archives a validation suite for MMFF94s.  As described in a paper just out
(T. A. Halgren, J. Comput. Chem., 20, 720-729 (1999)), MMFF94s differs from
MMFF94 in that it employs modified parameters that serve to make trigonal
delocalized nitrogens in structures such as amides, enamines, anilines, and
nucleotide bases planar or nearly so.  As a result, energy-optimized MMFF94s
structures resemble common experimentally determined structures, such as
X-ray
structures, much more closely than do optimized MMFF94 structures; such
experimental structures reflect time-averaged atomic coordinates in addition
to the effects of condensed-phase interactions that theoretical calculations
show also promote planarity at nitrogen.

The suite contains a README file (or, for Web browsers, its html equivalent)
that defines the files in the validation suite.  The most important are:

MMFF94s_dative.mol2                 mol2-format input, using dative bonds
for
                                                         certain sulfur and
phosphorous compounds

MMFF94s_hypervalent.mol2      SYBYL mol2 input, using "hypervalent"
                                                         representations

MMFF94s.mmd                             BatchMin/MacroModel dat-format input

MMFF94s.energies                      list of BatchMin and Merck-OPTIMOL
total
                                                         energies

MMFF94s_bmin.log                     BatchMin output log file

MMFF94s_opti.log                       OPTIMOL output file with detailed
                                                        interaction analyses

These input and output files provide data for the validation suite, which
consists of the 235 molecules in the 761-membered MMFF94 validation suite
for which MMFF94 and MMFF94s give different results.

Most of the input data is derived from CSD structures.  I wish to thank
Steve Salisbury and the Cambridge Crystallographic Data Center for
graciously consenting to the use of this data.  I also wish to thank Jan
Labanowski for his encouragement in the posting of this validation suite and
for his role in providing CCL and its archives to the community.

My hope is that this data will assist members of the community who wish to
implement MMFF94s to validate their efforts.

This validation suite is also intended allow individuals who use an
independently developed commercial implementation of MMFF94s to carry out
their
own validation and to satisfy themselves as to its authenticity.

The MMFF94s validation suite can be accessed at:

      http://www.ccl.net/cca/data/MMFF94s

      http://server.ccl.net/cca/data/MMFF94s

      ftp://ftp.ccl.net/pub/chemistry/data/MMFF94s

or via anonymnous ftp at:

      ftp.ccl.net; cd to pub/chemistry/data/MMFF94s.

The corresponding MMFF94 validation has the same address but without the
final "s".

I would be pleased to hear of any use made of this data.

                                                        Best regards,

                                                        Tom Halgren

                                                        voice: 732-594-7735
                                                        fax: 732-594-4224
                                                        [email-masked]