From muem@iuct.fhg.de Fri Dec 13 06:09:20 1996 Received: from fhg.de for muem@iuct.fhg.de by www.ccl.net (8.8.3/950822.1) id FAA26803; Fri, 13 Dec 1996 05:56:42 -0500 (EST) Received: by mailgw1.fhg.de (fhg.de); Fri, 13 Dec 1996 11:56:28 +0100 (MET) X-ENV: (fhg.de) muem@iuct.fhg.de -> CHEMISTRY@www.ccl.net.VIA-SMTP Received: by mailgw1.fhg.de (fhg.de) with SMTP; Fri, 13 Dec 1996 11:56:24 +0100 (MET) from iuct.fhg.de Received: by iuct.fhg.de; Fri, 13 Dec 96 11:56:52 +0100 from 153.96.228.113 (iuct113.iuct.fhg.de) From: "Martin Mueller" Message-Id: <961213115625.ZM16087@153.96.228.113> Date: Fri, 13 Dec 1996 11:56:22 +0200 X-Mailer: Z-Mail 4.0.1 (4.0.1 Apr 9 1996) To: CHEMISTRY@www.ccl.net Subject: SMILES -> 2D-Structure ? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, I am looking for a software tool (Windows 3.1, DLL or VBX) for converting SMILES-code into 2-dimensional structure. This tool should be able to visualize the struture and to save it as molfile (or maybe another common format). The tool should be usable together with Visual Basic and I need a distribution license. Best wishes for Christmas to all Martin Mueller -- Dr. Martin Mueller Fraunhofer-Institute for Environmental Chemistry and Ecotoxicology P.O.B. 1260, D-57377 Schmallenberg Phone: *49-2972-302 227 FAX: *49-2972-302 319 Internet: http://www.iuct.fhg.de From tamasgunda@tigris.klte.hu Fri Dec 13 07:09:22 1996 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.8.3/950822.1) id GAA26888; Fri, 13 Dec 1996 06:27:54 -0500 (EST) Message-Id: <199612131127.GAA26888@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Fri, 13 Dec 1996 12:27:47 EST Comments: Authenticated sender is X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Fri, 13 Dec 1996 12:27:44 +1 Subject: HIV-protease picture wanted Reply-To: tamasgunda@tigris.klte.hu Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Hi Netters, I am just writing a lecture book on drug chemistry & mechanisms of drug action for students, for in-house use only. I would like to insert a picture of the symmetrical HIV-1 protease with a fitted peptide-like protease inhibitor. If somebody could send me one in any known molfile format, it would be greatly appreciated. best wishes Tamas Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From Mark@synopsys.co.uk Fri Dec 13 10:09:22 1996 Received: from relay-11.mail.demon.net for Mark@synopsys.co.uk by www.ccl.net (8.8.3/950822.1) id JAA27870; Fri, 13 Dec 1996 09:56:47 -0500 (EST) Received: from sss1.demon.co.uk ([158.152.53.65]) by relay-9.mail.demon.net id ab916954; 13 Dec 96 14:46 GMT Date: Fri, 13 Dec 1996 15:08:44 GMT From: Mark Reply-To: Mark@synopsys.co.uk Message-Id: <3480@synopsys.co.uk> To: CHEMISTRY@www.ccl.net Subject: SMILES -> 2D Structure X-Mailer: FIMail V0.9d Lines: 26 Dear CCLers, In response to the mail message from Dr Martin Mueller of 13th December. Synopsys Scientific Systems Ltd develops a software tool (Windows 3.1, DLL or VBX) for converting SMILES-code into 2-dimensional structure. For further information visit our WWW site: http://www.synopsys.co.uk/ Have a good christmas Mark G Vero -------------------------------------------------------------------------------- Mark G Vero Synopsys Scientific Systems Ltd 175 Woodhouse Lane, Leeds, LS2 3AR, United Kingdom E-Mail: mark@synopsys.co.uk Tel: +44 (0) 113 245 3339 Fax: +44 (0) 113 243 8733 -------------------------------------------------------------------------------- From drbevan@vt.edu Fri Dec 13 10:16:33 1996 Received: from quackerjack.cc.vt.edu for drbevan@vt.edu by www.ccl.net (8.8.3/950822.1) id JAA27849; Fri, 13 Dec 1996 09:54:54 -0500 (EST) Received: from sable.cc.vt.edu (sable.cc.vt.edu [128.173.16.30]) by quackerjack.cc.vt.edu (8.7.1/8.7.1) with SMTP id JAA13288 for ; Fri, 13 Dec 1996 09:54:53 -0500 (EST) Received: from [128.173.82.100] (bevan.biochem.vt.edu [128.173.82.100]) by sable.cc.vt.edu (8.6.12/8.6.12) with SMTP id JAA20182 for ; Fri, 13 Dec 1996 09:54:52 -0500 X-Sender: drbevan@mail.vt.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Dec 1996 09:54:40 -0500 To: chemistry@www.ccl.net From: drbevan@vt.edu (David Bevan) Subject: Molecular Visualization on SUNs I teach a graduate-level course entitled "Molecular Modeling of Proteins and Nucleic Acids". This year for the first time I have access to a UNIX classroom that is equipped with 8 Sun Sparc 20 workstations. I am aware of programs that run on Sun workstations to do the number crunching (e.g., AMBER, MOPAC). However, I have been unable to find a program that will allow building and visualization of molecules on Sun workstations. I could probably use Rasmol for visualizing macromolecular structures for which coordinates are available. However, I also need a program that will enable us to build and visualize small molecules. Of course, cost is an object so I am hoping for something that is made available to universities for nominal costs. Does anyone have any suggestions based on their experience with Sun workstations? David Bevan ********************************************** * Dr. David R. Bevan * Dept. of Biochemistry * Virginia Polytechnic Institute & State University * Blacksburg, VA 24061-0308 * Telephone: (540) 231-5040 * FAX: (540) 231-9070 ********************************************** From kelterer@fptchbds01.tu-graz.ac.at Fri Dec 13 11:09:26 1996 Received: from fptchbds01.tu-graz.ac.at for kelterer@fptchbds01.tu-graz.ac.at by www.ccl.net (8.8.3/950822.1) id KAA28222; Fri, 13 Dec 1996 10:26:40 -0500 (EST) Received: by fptchbds01.tu-graz.ac.at (5.57/Ultrix3.0-C) id AA25406; Fri, 13 Dec 96 17:25:53 +0100 Date: Fri, 13 Dec 96 17:25:53 +0100 From: kelterer@fptchbds01.tu-graz.ac.at (M.Kelterer) Message-Id: <9612131625.AA25406@fptchbds01.tu-graz.ac.at> To: chemistry@www.ccl.net Subject: answers-MMFF94-distribution Answers to my question > I'd like to use the program MMFF94 > -- either in BatchMin version 5.5 from Clark Still's group > -- or the earlier Cerius2 implementation of MMFF93 from MSI. > > Who can help me with the email- or fax-adress of the group > who is distributing these programs, the costs > of the programs and/or experience with performance, > handling, etc ? 1) I can answer a related question; MMFF has been added to the c25 version of CHARMM, which is distributed by the Karplus group at Harvard (for a modest fee; a few hundred dollars, I believe). See http://yuri.harvard.edu -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov \/ |=| position of the FDA; for that, http://nmr1.cber.nih.gov/venable.html |=| see http://www.fda.gov ) 2) This was a very good information, costs of MacroModel/Batchmin are us$ 1000. for a single academic license. AMK. Hello, Please see the URL below for info about MacroModel/Batchmin. You can write to us at "mmod@still3.chem.columbia.edu" for further information. -P. -- ************** Watch this space for an important message... *************** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** MacroModel WWW page: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html 3) From richard@tc.cornell.edu Wed Dec 4 18:43:48 1996 I would like to know this as well. Could you forward the info to me too? Thanks ps. We are developing a C++ class library for automatic assignment and energy evaluation of MMFF94. It will be integrated into a flexible ligand docking code being developed at University of Alberta Canada (but also available as a library). The authors of the docking code are planning on offering a workshop with me (here at Cornell) tentatively scheduled for late April 1997. We will post an official announcement on CCL some time in late January. Richard Gillilan Cornell Theory Center --- Thank you all Anne-Marie KElterer. From aholder@cctr.umkc.edu Fri Dec 13 12:09:30 1996 Received: from axp2.umkc.edu for aholder@cctr.umkc.edu by www.ccl.net (8.8.3/950822.1) id LAA28634; Fri, 13 Dec 1996 11:11:34 -0500 (EST) Received: from 134.193.11.2 by axp1.umkc.edu (MX V4.1 AXP) with SMTP; Fri, 13 Dec 1996 10:10:54 CST X-Mailer: InterCon tcpCONNECT4 4.0.2 (Macintosh) MIME-Version: 1.0 Message-ID: <9612131011.AA30595@134.193.11.2> Date: Fri, 13 Dec 1996 10:11:30 -0600 From: "Andy Holder" To: chemistry@www.ccl.net Subject: Re: CCL:AM1/PM3/MNDO parameters for Fe and Ni? Content-Type: Multipart/Mixed;boundary=part_AED6DC520006D83F00000003 --part_AED6DC520006D83F00000003 Content-Type: Text/Plain; charset=US-ASCII Content-Disposition: Inline Netters, In reply to: > A colleague of mine is looking for semiempirical parameters (AM1,PM3 > and/or MNDO) for Fe and Ni. I already searched the CCL archives but > the only thing I found were similar questions... no answers. I have seen this question asked a number of times (and with increasing frequency) in the last months. I wanted to take a moment to explain why there are no good answers to this exact question and what the alternatives are. The currently popular Dewar-style methods (MNDO, AM1, and PM3) are not suited in their original incarnations for treating transition metals. This is simply because the original formulation of these models did NOT contain d-orbitals. The main group elements can be handled because the valence shells are only s and p. (Note that Zn, Cd, and Hg are also treatable because they have closed d-shells and can be treated as basic s2 elements.) (It is correct that d-functions are needed for proper treatment of these elements at the ab initio level (and perhaps the semiempirical as well!), but we are focusing on actual orbitals here, not polarization functions. There has been quite a lively debate in the literature about the actual role of these functions in hypervalent main group elements. This focuses on whether they act as mere polarization functions or actually particiapte in bonding in keeping with an sp3d2 hybridization idea.) Now, how do we get around this? There are two basic schools of thought: 1. Extend the multipole expansion (ME, the technique used to compute two- electrons repulsion integrals (TERIs)) to d-orbitals. This has advantages, in that it is very fast and we can take advantage of previous parameters. This was the approach pioneered by Walter Thiel and coming to fruition in the so- called MNDO/d method (available now in Unichem and soon in AMPAC and other places). This treatment was extended to PM3 and I believe AM1 by some people at Wavefunction (found in Spartan). It should be noted with some caution that these elements were parameterized with reference ONLY to X-ray geometries of closed-shell molecules. Traditionally, gas-phase heats of formation, ionization potentials, dipole moments, and geometries are used to give a balanced picture of a variety of properties, resulting in a general method. MNDO/d References: Thiel, W.; Voityuk, A. A. Theor. Chim. Acta 1992, 81, 391. Thiel, W.; Voityuk, A. A. Intl. J. Quant. Chem. 1993, 44, 807. Thiel, W.; Voityuk, A. A. THEOCHEM 1994, 313, 141. Thiel, W.; Voityuk, A. A. J. Phys. Chem. 1996, 100, 616. Thiel, W. Adv. Chem. Phys. 1996, 93, 703. 2. Scrap the ME and use something different. This was the approach taken in the Dewar group and followed up in my group with SAM1 and (hopefully) its successors. Here we used a simplified set of Gaussian orbitals that are semiempirically scaled for computing TERIs. This gives a different method of computing these quantities, one that we hope is better. It should also be noted that this approach requires a COMPLETE reparameterization of the methods. This is both good and bad. "Bad" because it is a great deal of work, but "good" because the older parameters were derived in times of much more limited computer resources. We can now afford to do MUCH more extensive searches than previously and use larger molecules and basis sets of systems for parameterization than ever before! This is SAM1 and it is currently found in our AMPAC. SAM1 References: Dewar, M. J. S.; Jie, C.; Yu, G. Tetrahedron 1993, 23, 5003. Holder, A. J.; Dennington, R. D.; Jie, C. Tetrahedron 1994, 50, 627. Holder, A. J.; Evleth, E. M. in Modeling the Hydrogen Bond; Smith, D. A.; American Chemical Society, Washington, DC,1994; pp 113. Currently work is going on in several places (including here and in Professor Thiel's lab) to complete these methods for more of the periodic table. Stay tuned. I should also note that ZINDO (M. Zerner, U. of Florida) has been available for quite some time and handles these elements, but has some constraints. Also, one can always do ab initio (standard basis sets exist) or DFT. Hope that this helps. Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- UUUU UUU MMM MMKK KKKK CCCC | ANDREW J. HOLDER UU U MM MMK K CC CC | Assoc. Prof. of Comp./Org. Chemistry UU U MMM M MK KK CCC | Dept. of Chemistry UU U M MM MK KK CC CC | University of Missouri-Kansas City UUUUU MMM M MMKK KK CCCC | Kansas City, MO 64110 KK | aholder@cctr.umkc.edu K | (816) 235-2293, FAX (816) 235-5502 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- --part_AED6DC520006D83F00000003-- From raman@bioc01.uthscsa.edu Fri Dec 13 13:09:24 1996 Received: from elzip.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.8.3/950822.1) id MAA29481; Fri, 13 Dec 1996 12:39:36 -0500 (EST) Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V5.0-5 #13300) id <01ICYKEPYM7400BNUB@uthscsa.edu>; Fri, 13 Dec 1996 11:31:37 -0600 (CST) Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V5.0-5 #13300) id <01ICYKENVV8600BO5E@uthscsa.edu>; Fri, 13 Dec 1996 11:31:32 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA04226; Fri, 13 Dec 1996 11:34:04 -0600 (CST) Date: Fri, 13 Dec 1996 11:34:04 -0600 (CST) From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Subject: Re: CCL:M:Molecular Visualization on SUNs In-reply-to: To: drbevan@vt.edu (David Bevan) Cc: chemistry@www.ccl.net Message-id: <9612131734.AA04226@bioc01.uthscsa.edu> X-Mailer: ELM [version 2.4 PL3] Content-type: text Content-transfer-encoding: 7BIT David: > I am hoping for something that is made available to universities for > nominal costs. Does anyone have any suggestions based on their experience > with Sun workstations? I would recommend the program XTALVIEW (written by Duncan McRee, Scripps Research Institute) which runs on SUN platforms without any problem. It run under the X11 environment and is quite good for manipulating coordinates, visualization etc. It is a full-fledged system for solving crystal structures, but, will suffice your needs and easy to use. It is distributed by San Diego Super Computer Center (SDSC) at no cost to you. A license agreement, however, needs to be signed. For more information, please ftp to sdsc.edu and look at /pub/ccms/README. Alternatively you can check out www.sdsc.edu. Cheers -raman ______________________________________________________________________ C.S.Raman Tel: (210) 614-0839 Dept. of Biochemistry Fax: (210) 567-2490 University of Texas email:raman@bioc01.uthscsa.edu Health Science Center 7703 Floyd Curl Drive San Antonio, TX, 78284-7760 U.S.A. ---------------------------------------------------------------------- The real problem in speech is not precise language. The problem is clear language. --Richard Feynman ______________________________________________________________________ From jeff@elmer.bnpi.com Fri Dec 13 15:09:24 1996 Received: from beavis.bnpi.com for jeff@elmer.bnpi.com by www.ccl.net (8.8.3/950822.1) id OAA00309; Fri, 13 Dec 1996 14:13:11 -0500 (EST) Received: from elmer.bnpi.com (elmer [198.213.32.6]) by beavis.bnpi.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id NAA03513 for <@beavis.bnpi.com:chemistry@www.ccl.net>; Fri, 13 Dec 1996 13:10:40 -0700 Received: (from jeff@localhost) by elmer.bnpi.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) id NAA03589 for chemistry@www.ccl.net; Fri, 13 Dec 1996 13:10:03 -0600 Date: Fri, 13 Dec 1996 13:10:03 -0600 From: jeff@elmer.bnpi.com (Jeff D. Saxe) Message-Id: <199612131910.NAA03589@elmer.bnpi.com> To: chemistry@www.ccl.net Subject: summary of plot program for EHT MOs I recently posted the following question: > We are looking for a program which will plot 2D MO contours from > extended Huckel calculations. We need a program which can handle > d-orbitals. I received a number of replies, all of which said to try either HyperChem or CACAO. For HyperChem info you can send mail to info@hyper.com or go to hhtp://www.hyper.com. For CACAO (which appears to run only on a PC) you can download it from: ftp: ftp.area.fi.cnr.it login: anonymous password: your e-mail address. the contents of the cacao ftp-anonymous are in the directy: /pub/issecc and its subdirectories. In particular the package CACAO40.exe is in: /pub/issecc/cacao Here is the beginning of the README.1ST file for CACAO: *********************************************************************** * * * C A C A O * * ========= * * Computer Aided Composition of Atomic Orbitals * * (A Package of Programs for Molecular Orbital Analysis) * * [PC Version 4.0, 1994] * * * * CARLO MEALLI and DAVIDE MARIA PROSERPIO * * * * Symmetry routines written by KLAUS LINN (1991) * * Revisions made by Angelo Sironi and Jose A. Lopez (1992) * * Version Compiled with Microsoft Fortran Powerstation which * * overcomes the limitations of DOS 640 Kb. * * New Options allow to examine the results of many different * * calculations in a single interactive CACAO session. * * (Mealli 1993) * * * *********************************************************************** * Reference: Journal of Chemical Education 1990, (67), 399-402 * *********************************************************************** The present file (README.1ST) illustrates the installation and the gross features of the program CACAO. More details are contained in the file MANUAL which can be found in the directory MOAN after a successfull installation. MANUAL is provided in different formats: 1) MANUAL.TXT (ascii file) 2) MANUAL.PS (PostScript) 3) MANUAL.DOC (WinWord2.0 Document) *********************************************************************** How to retrieve, install and get acquainted with CACAO: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CACAO is a multipurpose EHMO package with graphical interface written and distributed by: Drs. Carlo MEALLI and Davide M. PROSERPIO CACAO consists mainly of two programs (EHC.exe for EHMO calculations and CACAO.exe (for interactive analysis) The present version CACAO4.0 (July 1994) has many new improvements with respect to the previous ones. Compiled with Fortran Powerstation (V 1.0) by Microsoft, it allows to bypass the limit of DOS 640K, the limit being now given by the physical memory available in your computer and by the maximum array dimensions for atoms (125) and orbitals (500). Among the many features, CACAO offers the possibility of analyzing many different datasets (from different EHMO calculations) in a single interactive session for comparative purposes. The quality of the drawings and the speed to generate them is now improved. The hard copy of any drawing on the screen can be obtained in real time with a single key-stroke. The whole CACAO package is contained in the file cacao40.exe, available via FTP by logging at 149.139.10.2 (cacao.issecc.fi.cnr.it) as anonymous (use your e-mail as password). Get the file in the binary mode. Thanks to everyone who responded. Jeff Saxe