From chemistry-request@server.ccl.net Mon Apr 26 19:49:01 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA08206 for ; Mon, 26 Apr 1999 19:49:01 -0400 Received: from mgw2.merck.com (mgw2.merck.com [155.91.4.103]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA08754 Mon, 26 Apr 1999 19:44:27 -0400 (EDT) Message-Id: <199904262344.TAA08754@www.ccl.net> Date: Mon, 26 Apr 1999 19:42:16 -0400 From: "Halgren, Thomas" Subject: Validation suite for MMFF94s (see J. Comp. Chem., May 1999 issue) To: "'Computational Chemistry List'" Cc: "'Labanowski, Jan'" MIME-version: 1.0 Content-type: text/plain Content-transfer-encoding: 7BIT 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 halgren@merck.com