THIS INFORMATION IS OBSOLETE AND IS PROVIDED ONLY FOR ITS HISTORICAL VALUE

MM3(96) MM3(96) ANNOUNCMENT Effective immediately, the MM3(96) system is available for distribution. There will be differences between the distribution of this latest version of the system and earlier versions. Whereas in earlier versions source code was being distributed, this is no longer being done. Beginning with MM3(94) the system will be distributed in the form of executable code and object code. In addition to signing and returning a Use Agreement, it will be necessary for the user to obtain a special password from QCPE in order to make the system operable. The password will be based in the ID number of your computer. This information will be used to generate the password. This will have the effect of limiting the use of MM3(94) to a single computer. At present time the following versions of the system are available: IBM RS/6000 (aix) Silicon Graphics (irix) Digital Alpha (osf) DEC workstation (ultrix) PC running under LINUX At this time QCPE is distributing the IBM and the Silicon Graphics versions. If you need one of the other versions, please contact QCPE. Two separate versions of the system are delivered in each order. There is a 1000 atom version and also a 2000 atom version. We can deliver either by ftp or on a 150 Mb tape cartridge. There have been major additions to this system since the MM3(92) version. MM3(96) contains a Molecular Dynamics module. It also has a code which can automatically estimate parameter values in those cases in which official parameters are missing. On the order sheet supplied on the back of this announcement, be certain to supply the type of computer you are using and the ID for your computer. To obtain the ID number which we need to generate the password on the Silicon Graphics or IBM RS/6000 do one of the following: Silicon Graphics: /etc/sysinfo -s (gives 10 digits) IBM RS/6000: uname -m (gives 12 digits) The total cost, delivered in the U.S. is $700.00. Checks should be made payable to "IU Foundation/QCPE". --Richard W. Counts QCPE

New in MM3(96) New Features. There are two new major additions to this version of the program. (a) A new treatment for Coordination compounds is added. This is in addition to the other two treatments, which remain unchanged. With the new treatment, the metal atom (M) will be treated like any normal atom with the following exceptions: Up to 20 attached atoms are allowed. All ligand donor atoms (L) that are attached directly to the metal atom (M) have van der Waals interactions between them (with 1,3 VDW interactions). All L-M-L bends are removed from the interaction list. All X-M-L-X torsions are removed from the interaction list. All stretch-bend terms that involve M-X-X or X-M-X are removed. All bend-bend terms that involve M-X-X or X-M-X are removed. Note: Metal atoms that may be treated with this new treatment are flagged with "-1" in the atom type definition section (column CRD) of the program default parameter file (CONST.MM3). To use a metal atom other than a default atom, the user has to modify CONST.MM3 file. This method of treating coordination compounds seems more simple and generally usefull than earlier methods. (b) The Torsion-Stretch term has been extended from three-fold (V3) only to include V1, V2 and V3 terms. This change gives MM3 more control over the Torsion-Stretch interaction in some complicated system, such as hydrazine. Note: The input format for the use of the torsion-stretch parameter has been changed to match the new equation. Improvements and Corrections. Other significant improvements and corrections are, The default maximum number of VESCF interactions to be run in attempting to reach self consistency is increased from 8 to 12. This change will allow the VESCF energy to be further minimized in each VESCF cycle. The maximum atomic movement restriction during the minimization (both block-diagonal and full-matrix methods) has been reduced from 0.25 to 0.10 A. The change helps th minimization keep on course, and will avoid unexpected atomic movement fluctuations on some complicated energy surfaces (the 0.25 A was inherited from MM2 program.) nnI particular, the program now runs to completion without the "energy has gone up" message in all cases. Bond length conversions among rg, ra and rz have been modified to improve the accuracy of the calculations relative to the standard literature procedures. The rs bond length conversion has also been added into the program. New Parameters that have been added to MM3(96) Directional hydrogen bonding part II. For C,N,O Cl systems, including formamide dimer and formamide-water complex.---- J.-H. Lii, Paper in preparation Sulfoxides---N. L. Allinger, Y Fan, and T. Varnali, J. Phys. Org. Chem., 9, 159 (1996) Alkynes & Nitriles---- C. Goldstein , B. Ma, J.-H. Lii, and N. L. Allinger, J. Phys. Org. Chem.,9, 191 (1996). Hydrazines --- B. Ma, J.-H., Lii, K. Chen, and N. L. Allinger, J. Phys. Chem., 100, 11297 (1996). Silanes ---- K. Chen and N. L. Allinger, submitted to J. Phys. Org. chem.chem.uga.edu (Allinger)) wrote: Chem. Imminiums & Pyridium ---- Non-conjugated systems: G. B. McGaughey, E. L. Stewart, and J. P. Bowen, J. Comput. Chem., 16, 1250 (1995). Conjugated systems: G. B. McGaughey, E. L. Stewart, and J. P. Bowen, J. Comput. Chem., 17, 1395 (1996). Sulfonamides ---- G. Y. Liang, J. P. Bays, and J. P. Bowen, J. Mol. Struct. (Theochem.), in press. Boronic acids ---- X. Chen, G. Y. Liang, D. Whitmire, and J. P. Bowen, J. Phys. Org. Chem., submitted. Ammonium ion & protonated polyamines--- G. Y. Liang, X. Chen, J. A. Dustman, A. H. Lewin, and J. P. Bowen, J. Comput. Chem.., submitted. Alkyl fluorides--- G. Walker, paper in preparation.

MM3(96) Upgrade Policy If you purchased the MM3(94) system during calendar year 1996 or during 1997 you qualify to receive a free copy of the MM3(96) system. The only proviso is that you pick up the system from our computer over the internet. When applying to take advantage of the above arrangement please give us the approximate date when you obtained the MM3(94) system. If you purchased MM3(94) prior to calendar year 1996 the upgrade price is $200.00 with the only proviso being that you pick up the system from our computer over the internet. These arrangements are possible because the MM3(94) documentation which you now have remains valid with the addition of the information which is contained in the file "MM3(96)_Now_Available". In the case of any other situations which are not covered in this policy please contact QCPE directly. ---Richard W. Counts/QCPE

PC Version of MM3(96) Now Available Previously there have been versions of the MM3 series of programs available for the IBM RS/6000, the Silicon Graphics platforms and the DEC alpha machines. To date there has been no generally available PC version of this system. Effective immediately there is now a version of the MM3(96) system available for PCs running under the unix-like operating system Linux. The system will be distributed in executable format (a.out format) and will require 10 Mb of virtual memory to execute. A password file will also be required. As PCs do not have computer ID numbers like workstations the Ethernet Card ID is being used in its place. So in order to use this new version of the MM3(96) system you must have a PC which contains an Ethernet Card and which is running under Linux. As with any order for the MM3 system the individual making the order must supply us with this Ethernet Card ID number. This number should look as follows: 00:00:00:03:75:0E (typical example) This number can be generated under the Linux system by giving the following command: /sbin/ifconfig | grep HWaddr Once QCPE has a signed license and the above information we can proceed immediately to fill an order. We usually prefer to set up orders in the form of compressed tar files which can be quickly downloaded from our computer. ---Richard W. Counts/QCPE

MM3(96) USE AGREEMENT The system MM3(96) is not a normally distributed QCPE program. It is being distributed under a special agreement with Prof. N. L. Allinger of the University of Georgia. The conformational search subroutine used in MM3(96) is used with permission of Yale University, which is the holder of patent 4,855,931. This is the patent which covers the minimization procedure. The terms of this agreement permit QCPE to distribute MM3(96) to academic institutions only. Distribution to all other clients is being handled by TRIPOS Assoc. Inc. of St. Louis, Missouri. The recipient of this system also receives it with certain restrictions: 1. If modifications of this system are required in the course of research and the results of this research are subsequently published, the publication MUST state clearly what these modifications entail. 2. The recipient of this system may not redistribute it to other users in either its original or modified form. Upon receipt of the attached agreement signed by the researcher and in conjunction with an appropriate purchase order, QCPE can ship promptly. In order to be certain that everyone is aware of these restrictions, we now require that anyone ordering MM3(96) sign the enclosed form. --Richard W. Counts MM3(96) USE AGREEMENT I am aware of the following restrictions: 1. If modifications of this system are required in the course of research and the results of this research are subsequently published, the publication MUST state clearly that modifications have been made and describe exactly what these modifications entail. 2. The recipient of this system may not redistribute it to other users in either its original or modified form. QCPE warrants that the magnetic media on which the program code is contained shall be free from defects and workmanship and manufacture for a period of ninety (90) days from the day of the license. Except as provided in the preceding sentence, LICENSEE acknowledges that QCPE makes no warranty, expressed or implied, that the program will function without error, or in any particular function or result, and further excluding any other warranty, as to the condition of the program, its merchantability, or its fitness for a particular purpose. QCPE and N. L. Allinger shall not be liable for any direct, consequential or incidental damage suffered by the LICENSEE or any others as a result of their use of the program, whether or not the same could have been foreseen by QCPE or N. L. Allinger prior to granting this license. In no event shall QCPE or N. L. Allinger liability for any breach of this agreement exceed the fee paid for the license. This agreement applies to MM3(96). Please print or type the following information in the spaces following and return the entire document, signed, to QCPE: Date ___________________ Name of User ______________________________________________ Institutional Address ___________________________________ ___________________________________ ___________________________________ ___________________________________ Signature of User* ________________________________________ * This agreement must be signed by the ultimate user of MM3(96). No other agent is acceptable.

MM3(96) ORDER FORM Shipping Address_________________________________________ _________________________________________ _________________________________________ _________________________________________ Billing Address __________________________________________ __________________________________________ __________________________________________ __________________________________________ E-mail Address ------------------------------------------ Purchase Order No. ----------------------------------------- (or other means of payment) Computer Make & __________________________________________ Model Computer ID number ------------------------------------------ Method of Delivery ____ 150 Mb tape cartridge ____ Anonymous ftp pickup ____ ftp delivery In the case of ftp delivery, QCPE needs the following information: Internet address _____________________________________ Account name _____________________________________ Password_____________________________________ Printed documentation for this system will be shipped by UPS within the United States and Air Parcel Post to other destinations. Please remember to include a signed copy of the Use Agreement with this order.