Subject: Revised and extended MMFF94 Validation Suite

From: "Halgren, Thomas" <[email-masked]>
Date: Fri, 12 Feb 1999 09:44:44 -0500

Dear CCLers,

Jan Labanowski has kindly posted on the Computational Chemistry List
archives a revised and extended version of the MMFF94 Validation Suite that
was first released in May 1998. The new suite corrects MMFF94 results for
eight
structures for which the atom typing has been found to be erroneous, and adds
eight additional structures geared to more fully test the empirical-rule
parameter generation procedures defined in the published MMFF94 papers.

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:

MMFF94_dative.mol2 		mol2-format input, using dative bonds for
                                    		certain sulfur and
phosphorous compounds

MMFF94_hypervalent.mol2	SYBYL mol2 input, using "hypervalent"  
					representations

MMFF94.mmd 			BatchMin/MacroModel dat-format input

MMFF94.energies			list of BatchMin and Merck-OPTIMOL total
					energies

MMFF94_bmin.log			BatchMin output log file

MMFF94_opti.log 			OPTIMOL output file with detailed
					interaction analyses

MMFF94.changed-or-new_results 	Energies for new structures and for
						structures affected by corections to
the
						MMFF94 atom-typing procedures

MMFF94.empirical_rule_parameters	Listing of structures and
interactions for
						which empirical-rule parameters are
						generated

These input and output files provide data for the validation suite, which
now
consists of 761 molecules.

Also provided are auxiliary files that list the names of molecules that have
alternative dative and hypervalent representations (MMFF94.dative_molecules);
that specify the formal atomic charges used in the dative and hypervalent
representations (MMFF94.fc_dative and MMFF94.fc_hypervalent); and that list
the
molecule names and titles (MMFF94.titles).

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 have
independently implemented MMFF94, or who are in the process of doing so, to
validate their efforts (I am aware of five such initiatives, in addition to
the BatchMin and CHARMm implementations to which Merck has contributed).

Those who have already implemented MMFF94 should obtain and compare results
for
the corrected and added members of the validation suite, and should insure
that
any modifications they need to make do not affect the other members of the
suite.

This validation suite is also intended allow individuals who use an
independently developed commercial implementation of MMFF94 to carry out
their
own validation and to satisfy themselves as to its authenticity.

Those who are not interested in pursuing MMFF94 per se might view the suite
as a source of input data that could be useful in developing and testing
other force fields. A force-field evaluation suite comprised of ab initio
and/or experimental data on conformational energies and on intermolecular
interactions together with input molecular structure data is being posted
elsewhere on the CCL archives.  This suite may be even more useful for this
purpose.

The MMFF94 validation suite can be accessed at:

ftp://www.ccl.net/pub/chemistry/data/MMFF94

or at:

http://www.ccl.net/cca/data/MMFF94

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]