Subject: Validation suite for MMFF94 now available

From: "Halgren, Thomas" <[email-masked]>
Date: Mon, 01 Jun 1998 16:00:06 -0400

Dear CCLers,

Jan Labanowski has kindly posted on the Computational Chemistry List
archives a comprehensive validation suite for MMFF94 that I prepared.  The
suite contains a README file that defines all other files in the test suite.
The most important are:

MMFF94_dative.mol2		mol2-format input, using dative bonds for
oxysulfur, etc.
MMFF94_hypervalent.mol2	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

These input and output files provide data for the test suite, which consists
of 753 molecules.

There is also a subsidiary file that lists the names of molecules that have
alternative dative and hypervalent representations
(MMFF94.dative_molecules), and a file that just lists 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 four such initiatives, in addition to
the BatchMin and CHARMm implementations to which Merck has contributed); it
is always difficult to work from published accounts and to be sure you know
where you stand.  

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

Others 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.

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 uses made of this data.

							Best regards,

							Tom Halgren

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

---

From: John Marelius <[email-masked]>
Date: Tue, 2 Jun 1998 00:17:20 +0200 (MDT)

Dear CCLer,
if you happen to have a description of the format of mol2 files (used by
Sybyl and other software), please e-mail it to me.

John Marelius

+------------------------------------------------------------------------+
| 	   John Marelius                                                 |
| 	   Dept. of Molecular Biology, Uppsala University                |
| E-mail:  [email-masked]                                           |
+------------------------------------------------------------------------+