From kozelka@citi2.fr Tue Jan 13 04:14:54 1998 Received: from galaad.citi2.fr for kozelka@citi2.fr by www.ccl.net (8.8.3/950822.1) id DAA24917; Tue, 13 Jan 1998 03:26:46 -0500 (EST) Received: from bisance.citi2.fr by galaad.citi2.fr; (5.65/1.1.8.2/20Jun94-0455PM) id AA11237; Tue, 13 Jan 1998 09:30:49 +0100 Received: from crimson by bisance.citi2.fr (SMI-8.6/SMI-SVR4) id JAA18480; Tue, 13 Jan 1998 09:25:32 +0100 Sender: jirka@citi2.fr Message-Id: <34BB987F.41C6@bisance.citi2.fr> Date: Tue, 13 Jan 1998 08:38:23 -0800 From: Jirka Kozelka X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP17) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: ESP atomic charges from ADF? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL colleagues, I would like to use the electron density from an ADF calculation as input for a calculation of electrostatic potentials and for the determination of atomic charges by fitting the ESP from the monopoles to the ADF potential. Does anyone have an interface connecting ADF with a corresponding routine (e.g., the Merz-Kollman routine such as implemented in Gaussian94), or, do you have a hint where I could find it? Answers will be summarized and communicated. Thank you in advance. Jirka Kozelka -- *** Jirka Kozelka *** Universite Rene Descartes 45 rue des Saints-Peres F-75270 Paris 06 FRANCE Tel +331-42 86 21 75 Fax +331-42 86 83 87 e-mail kozelka@citi2.fr From mbskowro@cyf-kr.edu.pl Tue Jan 13 08:14:46 1998 Received: from info.cyf-kr.edu.pl for mbskowro@cyf-kr.edu.pl by www.ccl.net (8.8.3/950822.1) id HAA26164; Tue, 13 Jan 1998 07:59:32 -0500 (EST) Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.2.32]) by info.cyf-kr.edu.pl (8.8.8/8.8.8) with ESMTP id NAA22611 for ; Tue, 13 Jan 1998 13:58:32 +0100 (MET) Received: (from mbskowro@localhost) by kinga.cyf-kr.edu.pl (8.8.8/8.8.8) id NAA04441 for chemistry@www.ccl.net; Tue, 13 Jan 1998 13:58:02 +0100 (MET) Message-Id: <199801131258.NAA04441@kinga.cyf-kr.edu.pl> Subject: ion&basis set To: chemistry@www.ccl.net Date: Tue, 13 Jan 1998 13:58:01 +0100 (MET) From: Marek Skowronek X-Mailer: ELM [version 2.4ME+ PL37 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Netters, I would like to ask you two questions. 1. What is the most suitable basis set for a geometry optimization of an ion (35 atoms), which contain the SO3- group? 2. What is a spin for this molecule? Thank you in advance Marek Skowronek From desingh@syr.edu Tue Jan 13 12:14:59 1998 Received: from mailbox.syr.edu for desingh@syr.edu by www.ccl.net (8.8.3/950822.1) id MAA27686; Tue, 13 Jan 1998 12:11:43 -0500 (EST) Received: from dirac.syr.edu (syru33-128.syr.edu [128.230.33.128]) by mailbox.syr.edu (8.8.8/8.8.8) with SMTP id MAA07374 for ; Tue, 13 Jan 1998 12:11:44 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <34BBC24E.1CFB@syr.edu> Date: Tue, 13 Jan 1998 14:36:46 -0500 From: Deepak Singh X-Mailer: Mozilla 3.0SC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: computational chem list Subject: side-chain replacement program Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone, I am looking for a profram or package(preferably freeware), that can I can use to substitute various amino acids in a protein. I am planning to run some calculations on mutants and proteins with a lot of residue conservation. One way I could think of doing this would be to keep the backbone fixed and change side chains on prompting. Any suggestions? Thank you Deepak. ---------------------------------------------------------------------- Deepak Singh Graduate Student Department of Chemistry & W. M. Keck Center for Molecular Electronics Syracuse University Syracuse, NY 13244 Voice: (315) 443 5928, 443 1739 email:desingh@syr.edu Fax : (315) 443 4070 URL:http://web.syr.edu/~desingh ......the time is gone the song is over, thought I'd something more to say. Roger Waters in "time" ----------------------------------------------------------------------- From shenkin@still3.chem.columbia.edu Tue Jan 13 14:14:47 1998 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id NAA28350; Tue, 13 Jan 1998 13:35:23 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id NAA10551; Tue, 13 Jan 1998 13:35:20 -0500 (EST) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id NAA24376; Tue, 13 Jan 1998 13:35:20 -0500 From: "Peter Shenkin" Message-Id: <9801131335.ZM24374@still3.chem.columbia.edu> Date: Tue, 13 Jan 1998 13:35:19 -0500 In-Reply-To: Deepak Singh "CCL:side-chain replacement program" (Jan 13, 2:36pm) References: <34BBC24E.1CFB@syr.edu> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Deepak Singh , computational chem list Subject: Re: CCL:side-chain replacement program Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jan 13, 2:36pm, Deepak Singh wrote: > Subject: CCL:side-chain replacement program > I am looking for a profram or package(preferably freeware), that can I > can use to substitute various amino acids in a protein. I am planning > to run some calculations on mutants and proteins with a lot of residue > conservation. One way I could think of doing this would be to keep the > backbone fixed and change side chains on prompting. Any suggestions? > There are a number of programs -- commercial and academic -- that do this. For one of them, and a brief review of some of the others as of the publication date, see: Shenkin, Farid and Fetrow, "Prediction and Evaluation of Side-Chain Conformations for Protein Backbone Structures," Proteins, v.26, pp.323-352 (1996) (If you're interested in using "side", the program described there, let me know; the source code is freely available. But be warned: it's not terribly user-friendly.) Hope this helps, -P. -- ************ I have never seen even one episode of "Seinfeld." ************ * 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.columbia.edu/cu/chemistry/mmod/mmod.html * From pieter.stouten@dupontmerck.com Tue Jan 13 15:14:48 1998 Received: from gatekeeper.dupontmerck.com for pieter.stouten@dupontmerck.com by www.ccl.net (8.8.3/950822.1) id OAA28804; Tue, 13 Jan 1998 14:49:16 -0500 (EST) Received: by gatekeeper.dupontmerck.com; id OAA01433; Tue, 13 Jan 1998 14:49:12 -0500 (EST) Received: from unknown(158.117.31.71) by gatekeeper.dupontmerck.com via smap (3.2) id xma001431; Tue, 13 Jan 98 14:48:50 -0500 Received: from carbon.dmpc.com by DMPHUB.dmpc.com (PMDF V5.1-10 #24771) with ESMTP id <01ISBYP1PVY8001JDK@DMPHUB.dmpc.com>; Tue, 13 Jan 1998 14:48:49 EST Received: from [158.117.170.103] (esm170103.dmpc.com [158.117.170.103]) by carbon.dmpc.com (8.8.5/8.8.7) with ESMTP id OAA07611; Tue, 13 Jan 1998 14:48:48 -0500 (EST) Date: Tue, 13 Jan 1998 14:48:47 -0500 From: Pieter Stouten Subject: Re: CCL:side-chain replacement program In-reply-to: <34BBC24E.1CFB@syr.edu> X-Sender: stoutepf@carbon.dmpc.com To: chemistry@www.ccl.net Cc: gert.vriend@embl-heidelberg.de (Gert Vriend) Message-id: X-Organization: The DuPont Merck Pharmaceutical Company MIME-version: 1.0 X-Mailer: Eudora Pro 3.1 for Macintosh Content-type: text/plain; charset="us-ascii" On 98/01/13 at 14:36 -0500, Deepak Singh wrote: >I am looking for a profram or package(preferably freeware), that can I >can use to substitute various amino acids in a protein. I am planning >to run some calculations on mutants and proteins with a lot of residue >conservation. One way I could think of doing this would be to keep the >backbone fixed and change side chains on prompting. Any suggestions? > Try Whatif. It is free for academia. It can systematically replace individual residues and tell you how well the mutated residue fits into the rest of the structure (it does not optimize the structures when doing that, though). Contact Gert Vriend , Whatif's author, directly for more info. Good luck, Pieter Stouten DuPont Merck - Computer Aided Drug Design Group Web: http://www.halcyon.com/stouten/ From pieter.stouten@dupontmerck.com Tue Jan 13 16:14:53 1998 Received: from gatekeeper.dupontmerck.com for pieter.stouten@dupontmerck.com by www.ccl.net (8.8.3/950822.1) id PAA29087; Tue, 13 Jan 1998 15:23:11 -0500 (EST) Received: by gatekeeper.dupontmerck.com; id PAA01609; Tue, 13 Jan 1998 15:23:12 -0500 (EST) Received: from unknown(158.117.31.71) by gatekeeper.dupontmerck.com via smap (3.2) id xma001607; Tue, 13 Jan 98 15:22:44 -0500 Received: from carbon.dmpc.com by DMPHUB.dmpc.com (PMDF V5.1-10 #24771) with ESMTP id <01ISBZV3IODC001JFQ@DMPHUB.dmpc.com>; Tue, 13 Jan 1998 15:22:43 EST Received: from [158.117.170.103] (esm170103.dmpc.com [158.117.170.103]) by carbon.dmpc.com (8.8.5/8.8.7) with ESMTP id PAA08794; Tue, 13 Jan 1998 15:22:41 -0500 (EST) Date: Tue, 13 Jan 1998 15:22:40 -0500 From: Pieter Stouten Subject: Re: CCL:side-chain replacement program (revisited) In-reply-to: X-Sender: stoutepf@carbon.dmpc.com To: chemistry@www.ccl.net Cc: gert.vriend@embl-heidelberg.de (Gert Vriend) Message-id: X-Organization: The DuPont Merck Pharmaceutical Company MIME-version: 1.0 X-Mailer: Eudora Pro 3.1 for Macintosh Content-type: text/plain; charset="us-ascii" References: <34BBC24E.1CFB@syr.edu> On 98/01/13 at 14:48 -0500, I wrote: >Try Whatif. It is free for academia. > I just got set straight: in principle it is about $200 for academia to cover S&H, administrative overhead, etc. I think this is a one-time fee that entitles you to receiving future upgrades free of charge. Please contact Gert Vriend for the official word. Pieter Stouten || Computer Aided Drug Design Group || No good deed ever The DuPont Merck Pharmaceutical Company || goes unpunished P.O. Box 80500, Wilmington, DE 19880-0500 || Phone: +1 (302) 695 3515 || (Ferengi Rule Of Fax: +1 (302) 695 9090 || Acquisition #285) Internet: pieter.stouten@dupontmerck.com || Web: http://www.halcyon.com/stouten/ || From bowermj@mms.sbphrd.com Tue Jan 13 16:22:19 1998 Received: from ns01.sbphrd.com for bowermj@mms.sbphrd.com by www.ccl.net (8.8.3/950822.1) id PAA29214; Tue, 13 Jan 1998 15:50:28 -0500 (EST) Received: by ns01.sbphrd.com; id PAA05194; Tue, 13 Jan 1998 15:50:28 -0500 Received: from phinet.sbphrd.com(139.136.64.5) by ns01.sbphrd.com via smap (3.2) id xma005056; Tue, 13 Jan 98 15:50:09 -0500 Received: from phu868.um.us.sbphrd.com by phinet.sbphrd.com; (5.65v3.0/1.1.8.2/06Mar95-1250PM) id AA12379; Tue, 13 Jan 1998 15:50:08 -0500 Received: by phu868.um.us.sbphrd.com (951211.SGI.8.6.12.PATCH1042/940406.SGI) id PAA21011; Tue, 13 Jan 1998 15:50:08 -0500 From: bowermj@mms.sbphrd.com (Michael Bower) Message-Id: <199801132050.PAA21011@phu868.um.us.sbphrd.com> Subject: (Fwd) CCL:side-chain replacement program To: desingh@syr.edu, chemistry@www.ccl.net Date: Tue, 13 Jan 1998 15:50:08 -0500 (EST) Cc: rl_dunbrack@fccc.edu X-Mailer: ELM [version 2.4 PL25] Content-Type: text On Jan 13, 2:36pm, Deepak Singh wrote: > Subject: CCL:side-chain replacement program > I am looking for a profram or package(preferably freeware), that can I > can use to substitute various amino acids in a protein. I am planning > to run some calculations on mutants and proteins with a lot of residue > conservation. One way I could think of doing this would be to keep the > backbone fixed and change side chains on prompting. Any suggestions? SCWRL is a very fast and reliable option - I developed it in Fred Cohen's lab along with Roland Dunbrack. It uses a backbone-dependent rotamer library and a systematic search to place sidechains, and is non-stochastic. SCWRL was extensively tested against the entire database of known structures and in the course of constructing thousands of homology models. See Bower, Cohen, & Dunbrack, J. Mol. Biol. (1997) 267, 1268-1282. See www.cmpharm.ucsf.edu/~bower/scwrl/scwrl.html for more information and ordering info. SCWRL is free to academic researchers. Mike Bower Not speaking for SmithKline Beecham From ccl@www.ccl.net Thu Jan 8 06:13:40 1998 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id FAA26532; Thu, 8 Jan 1998 05:41:36 -0500 (EST) Received: from nessie.mcc.ac.uk for mbdtsnm@hpf.ch.man.ac.uk by bedrock.ccl.net (8.8.6/950822.1) id FAA02026; Thu, 8 Jan 1998 05:41:35 -0500 (EST) Received: from serenity.mcc.ac.uk by nessie.mcc.ac.uk with SMTP (PP); Thu, 8 Jan 1998 10:41:12 +0000 Received: from (hpf.ch.man.ac.uk) [130.88.12.28] by serenity.mcc.ac.uk with smtp (Exim 1.81 #4) id 0xqFOf-0001ET-00; Thu, 8 Jan 1998 10:41:09 +0000 Date: Thu, 8 Jan 1998 10:39:34 GMT Message-Id: <16004.9801081039@hpf.ch.man.ac.uk> From: "Nathaniel (noj) Malcolm" To: boufer@CeNNAs.nhmfl.gov Cc: chemistry@ccl.net In-Reply-To: (message from Ahmed Bouferguene on Tue, 30 Dec 1997 12:58:49 -0500 (EST)) Subject: Re: CCL:From X Y Z to YLM Reply-To: Noj.Malcolm@man.ac.uk ahmed, i'm not sure that this is entirely what you are looking for, but amongst other places Anthony Stone has tables for converting between cartesians and regular spherical harmonics in appendix E of his book "theory of intermolecular forces". you should be able to us ethese to get the conversions that you want. (if you can't get your hands on th ebook then the same tables are to be found in some of his papers and i can dig out the references if you need them) noj -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, Manchester. M13 9PL e-mail noj.malcolm@man.ac.uk From goto@msi.com Thu Jan 8 08:52:38 1998 Received: from mb101.infoweb.or.jp for goto@msi.com by www.ccl.net (8.8.3/950822.1) id IAA27174; Thu, 8 Jan 1998 08:05:26 -0500 (EST) Received: from [202.219.190.202] by mb101.infoweb.or.jp (8.8.7+2.7Wbeta7/3.6Wbeta6-09/12/97) id WAA03543; Thu, 8 Jan 1998 22:04:46 +0900 Message-Id: <199801081304.WAA03543@mb101.infoweb.or.jp> X-Sender: fwip5390@mb.infoweb.ne.jp X-Mailer: Macintosh Eudora Pro Version 2.1.4-Jr2 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" Date: Thu, 8 Jan 1998 22:05:15 +0900 To: "Hr. Dr. S. Shapiro" From: goto@msi.com (Narushi Goto) Subject: Re: CCL:? re WebLab 2.0 partial atomic charges Cc: chemistry@www.ccl.net, toukie@zui.unizh.ch Dear Dr. Shapiro, I am very sorry that we did not reply to you. My name is Narushi Goto. I am an application scientist of Teijin Molecular Simulations in Japan. The partial atomic charges of a given molecules are calculated using QEq (Charge equilibration method) based on this article. Rapp$B; (J A.K., Goddard, W.A., Charge Equilibration for Molecular Dynamics Simulations, J. Phys. Chem., 95, 3358, 1991 Regards, Naru At 4:04 PM 98.1.5, Hr. Dr. S. Shapiro wrote: > Dear Colleagues; > > Does anyone know how the partial atomic charges are calculated >using MSI's > WebLab 2.0? s it the Gasteiger-Marsili procedure, or is some other method > used? For a given molecule the WebLab 2.0 partial atomic charges are > quite different from the corresponding AM1 partial atomic charges. > Any relevant literature references are appreciated. > > (My e-letters to MSI on this matter have gone unanswered, so I >now bring > this question to the attention of the whole CCL community.) > > Thanks in advance to all responders, and to all CCL members a >very happy, > healthy, and successful 1998! > > Sincerely, > > S. Shapiro > toukie@zui.unizh.ch > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- ********************************************************** Narushi Goto Manager, Chief Scientist, A.R.S TMSI Science Office Sales & Marketing Division Molecular Simulations Inc. Teijin Molecular Simulations Inc. 9685 Scranton Road 2-17-8 Nihonbashi Hamacho San Diego, CA 92121-3752 Chuo-ku, Tokyo 103 JAPAN Phone:+1-619-546-5506 Phone:+81-3-3663-8615, 8525 Fax: +1-619-458-0136 FAX: +81-3-3663-8620 e-mail: goto@msi.com e-mail: goto@tmsi.co.jp URL: http://www.msi.com/ URL: http://www.tmsi.co.jp/ ********************************************************** From news@compchem.kiev.ua Thu Jan 8 14:13:51 1998 Received: from burka.carrier.kiev.ua for news@compchem.kiev.ua by www.ccl.net (8.8.3/950822.1) id OAA29920; Thu, 8 Jan 1998 14:02:36 -0500 (EST) Received: from sivka.carrier.kiev.ua (root@sivka.carrier.kiev.ua [193.193.193.101]) by burka.carrier.kiev.ua (8.8.6/8.Who.Cares) with ESMTP id VAA26339 for ; Thu, 8 Jan 1998 21:02:28 +0200 (EET) Received: (from uucp@localhost) by sivka.carrier.kiev.ua (8.8.7/8.8.7) with UUCP id UAA27976 for chemistry@www.ccl.net; Thu, 8 Jan 1998 20:58:06 +0200 (EET) Received: (from news@localhost) by netmaster.compchem.kiev.ua (8.7.6/8.6.9) id UAA29063; Thu, 8 Jan 1998 20:22:00 +0200 To: chemistry@www.ccl.net Path: news From: Andrey V Khavryutchenko Newsgroups: compchem.ccl Subject: SUMMARY: Ti and Fe parameters for semiempirical methods Date: 08 Jan 1998 20:21:55 +0200 Organization: Computational Chemistry Group Lines: 226 Sender: akhavr@compchem.kiev.ua Message-ID: NNTP-Posting-Host: netmaster.compchem.kiev.ua X-Newsreader: Gnus v5.4.37/XEmacs 19.15 Status: RO Content-Length: 7463 A month ago I've asked about semiempirical parameters for Ti and Fe elements. Sorry for the late summary, but, you know, there were a lot of holidays :) The original message: On 9 Dec 1997, Andrey V Khavryutchenko wrote: > > Hi, fellow compchemers! > > I am looking for Ti and Fe parameters for AM1/PM3/NDDO methods group. > CCL archives search resulted in one pointer to the WaveFunction, > Inc. ftp site, but it seems not providing them anymore. > > Can anyone share his parameters sets, links to those or just the > experience of calculation of Ti-and Fe-containing systems with > semiempirical methods. Note: I focus mainly on inorganic compounds. > > Thanks in advance. > -- > SY, Andrey V Khavryutchenko > Speaking only for myself There were a number of followups (the later two are the clarifications >from WaveFunction regarding the availability of parameters): Date: Tue, 16 Dec 1997 12:17:34 +0000 (GMT) From: John Waite Hi Andrey, For these elements you need a code that can deal with occupied d orbitals, like MNDO/d. Therefore see: W.Thiel and A.A.Voltyuk in TCA 81,(1992) 391, IJQC 44,(1992) 807 and J.Mol.Struct. 313,(1994) 141 I hope these help, John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* john@john1.eie.gr Organic and Pharaceutical Chemistry Institute, phone: ++30-1-7229811-5 X 1-810 Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6503131 c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece From: "Jianguo Yu" Date: Tue, 16 Dec 1997 09:14:31 -0800 On Dec 15, 3:37pm, Wayne Huang wrote: > > Hi, fellow compchemers! > > I am looking for Ti and Fe parameters for AM1/PM3/NDDO methods group. > CCL archives search resulted in one pointer to the WaveFunction, > Inc. ftp site, but it seems not providing them anymore. > > Can anyone share his parameters sets, links to those or just the > experience of calculation of Ti-and Fe-containing systems with > semiempirical methods. Note: I focus mainly on inorganic compounds. > > Thanks in advance. > -- > SY, Andrey V Khavryutchenko > Speaking only for myself We do have a method ( called PM3(TM) ) and parameters being able to calculate the Ti-and Fe-containing systems. If you need more information, please contact us or visit our web site( http://www.wavefun.com). Good luck! Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92612 | \/ | Lao-tzu (604-531 B.C.)| +-----------------------+------------------+-------------------------+ Date: Tue, 16 Dec 1997 16:39:41 -0600 From: "Andy Holder" --part_B0BC5F4D0001F48F00000001 Content-Type: Text/Plain; charset=US-ASCII Content-Disposition: Inline Dear Professor Khavryutchenko, In reply to: > I am looking for Ti and Fe parameters for AM1/PM3/NDDO methods group. > CCL archives search resulted in one pointer to the WaveFunction, Inc. > ftp site, but it seems not providing them anymore. > > Can anyone share his parameters sets, links to those or just > the experience of calculation of Ti-and Fe-containing systems > with semiempirical methods. Note: I focus mainly on inorganic > compounds. Our SAM1 method has Fe parameters. You can find oinfo about it on our web site at the address listed below. ******** Note New Address Below! ******** Best regards, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President Semichem, Inc. || Email: andy@semichem.com 7204 Mullen || Web: http://www.semichem.com Shawnee, KS, 66216 || Phone Number: (913) 268-3271 || Fax Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= --part_B0BC5F4D0001F48F00000001-- Date: Thu, 18 Dec 1997 09:59:16 -0700 From: shawn@wavefun.com (Shawn Butler) Subject: Re: Spartan 5.0.3 Cc: yu@wavefun.com Status: RO X-Status: Dear Dr. Yian: Hello again. Thanks for the note. The place on our web site is: http://www.wavefun.com/software/parameters/pm3all.html Sorry you had trouble finding this. Parameters are free for use with all of our software. Regards, Shawn Butler +--------------------------+--------------------+----------------------+ | (Mr.) Shawn C. Butler | ______________ | 18401 Von Karman | | Marketing Director / Web | \ __________/ | Suite 370 | | Wavefunction, Inc. | \ \\\\\\\\/ | Irvine, CA 92612 USA | | | \ \\\\\/ | | | shawn@wavefun.com | \ \\/ | Phone: (714)955-2120 | | | \/ | Fax: (714)955-2118 | +--------------------------http://www.wavefun.com----------------------+ Current Promotion(s): Buy Spartan 5.0 for HP Visualize workstation and get Spartan for $100 (U.S. Academic Only) "Who are you who are so wise in the ways of science?" From: "Wayne Huang" Date: Wed, 17 Dec 1997 14:31:52 -0800 On Dec 17, 11:19pm, Andrey V Khavryutchenko wrote: > Subject: Re: Titanium and iron parameters for semiempirical methods > On Tue, 16 Dec 1997, Jianguo Yu wrote: > > > We do have a method ( called PM3(TM) ) and parameters being able to calculate > > the Ti-and Fe-containing systems. If you need more information, please contact > > us or visit our web site( http://www.wavefun.com). > > Yes, I know, that Wavefunction has PM3(tm) parameters for > transition row metals, but there's no references to them on > your site. Or, if there is one, it is very difficult to > find them, since you don't have `search' feature. > > I'd like to know, if these parameters are available. And if > yes, are they free or cost money? > > Thanks. > > SY, Andrey V Khavryutchenko > > >-- End of excerpt from Andrey V Khavryutchenko The PM3(tm) reference has never been published. The PM3(tm) parameters must be used with PM3(tm) together, which at this point, is only available from Wavefunction. I can send you the Fe and Ti PM3(tm) parameters if you like. --Wayne -- +---------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemistry | Irvine, California 92612 | | Wavefunction, Inc. | 714-955-2120 <> 955-2118(fax)| | huang@wavefun.com | Web: http://www.wavefun.com | +---------------------------------------------------------------+ -- SY, Andrey V Khavryutchenko Speaking only for myself From goto@msi.com Fri Jan 9 06:13:52 1998 Received: from mb102.infoweb.or.jp for goto@msi.com by www.ccl.net (8.8.3/950822.1) id FAA04529; Fri, 9 Jan 1998 05:37:49 -0500 (EST) Received: from [202.219.191.31] by mb102.infoweb.or.jp (8.8.7+2.7Wbeta7/3.6Wbeta6-09/12/97) id TAA29599; Fri, 9 Jan 1998 19:37:48 +0900 Message-Id: <199801091037.TAA29599@mb102.infoweb.or.jp> X-Sender: fwip5390@mb.infoweb.ne.jp X-Mailer: Macintosh Eudora Pro Version 2.1.4-Jr2 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" Date: Fri, 9 Jan 1998 19:37:43 +0900 To: chemistry@www.ccl.net From: goto@msi.com (Narushi Goto) Subject: FYI: Novel prize winner was dead Dear Colleagues; Just for your information. Dr. Ken-ichi Fukui who is the Novel prize winner was killed by cancer this morning. Regards, Narushi Goto ********************************************************** Narushi Goto Manager, Chief Scientist, A.R.S TMSI Science Office Sales & Marketing Division Molecular Simulations Inc. Teijin Molecular Simulations Inc. 9685 Scranton Road 2-17-8 Nihonbashi Hamacho San Diego, CA 92121-3752 Chuo-ku, Tokyo 103 JAPAN Phone:+1-619-546-5506 Phone:+81-3-3663-8615, 8525 Fax: +1-619-458-0136 FAX: +81-3-3663-8620 e-mail: goto@msi.com e-mail: goto@tmsi.co.jp URL: http://www.msi.com/ URL: http://www.tmsi.co.jp/ ********************************************************** From N.Goldberg@tu-bs.de Fri Jan 9 07:13:54 1998 Received: from rzcomm1.rz.tu-bs.de for N.Goldberg@tu-bs.de by www.ccl.net (8.8.3/950822.1) id GAA04762; Fri, 9 Jan 1998 06:41:05 -0500 (EST) Received: from tu-bs.de (bonding.org-chem.nat.tu-bs.de [134.169.19.161]) by rzcomm1.rz.tu-bs.de (8.8.6/8.8.6) with ESMTP id MAA10351 for ; Fri, 9 Jan 1998 12:40:24 +0100 (MET) Message-ID: <34B60DFD.6A7D2994@tu-bs.de> Date: Fri, 09 Jan 1998 12:46:05 +0100 From: Norman Goldberg Organization: TU-Braunschweig X-Mailer: Mozilla 4.03 [de] (Win95; I) MIME-Version: 1.0 To: Computational Chemistry Subject: Summary: Visualization of Gaussian output under Win95 Content-Type: multipart/alternative; boundary="------------4048A47994E1F131C845CD56" Status: RO Content-Length: 9376 --------------4048A47994E1F131C845CD56 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Here's the summary of the answers I obtained concerning the visualization of G94 output under WIN95. Thanks to those who sent them! -Norman >Does someone out there know a convenient way to convert >Gaussian output files (on unix machines) into decent publishable >structures >that can easily be modified (labelled, etc.) under Win95 and >then imported into 'word'? --------------------------------------. I use Babel (free from the CCL archives) to convert more-or-less any common file format, including Gaussian, to a sybyl mol2 file. I then ftp that from the Unix system to my Mac and read it directly into Chem3D. Chem3D provides numerous annotation features and the resulting graphic can be directly imported into MS Word. You could do exactly the same under Windows. Hope this helps. George ============================================================================ George P. Ford | email: gford@smu.edu Department of Chemistry | web: http://www.smu.edu/~gford/ Southern Methodist University | telephone: (214)768-2479 Dallas, Texas 75275 | fax: (214)768-4089 ============================================================================ Try the Molden program obtainable from: http://www.caos.kun.nl/~schaft/molden/molden.html >From the freeware programs I've come across this is the best, but if you do come across any others more suitable for importing graphics into Windows applications, I'd appreciate the details. Best regards, Phil. ------------------------------------------------------- Phil Branton. Department of Chemistry, University of Surrey, Guildford, Surrey. GU2 5XH. Email: p.branton@surrey.ac.uk Tel: +44 (0)1483 259591 FAX: +44 (0)1483 259514 WWW: http://www.surrey.ac.uk/~chp2pb/ ------------------------------------------------------- This is not all that straight forward - but it works. Read the structure using Xmol and put out as XYZ. Read into Rasmol and make look nice, export at BMP (or gif , then use XV to make BMP). Read into Microsoft Paint and lable + touch up on a pixel by pixel basis (this works readly well). Copy onto clipboard. Past to Word. Good luck Alex -- ---------------------------------------------------------------------- | Dr. Alexander J Turner | | | Universitaet Zuerich |Tel.: (41)-1-6354239 | | Organisch-Chemisches Institut|Fax: (41)-1-6356812 | | Winterthurerstrasse 190 | | | CH-8057 Zuerich |E-Mail: turner@ocisgi28.unizh.ch | | Switzerland | | |----------------------------------------------------------------------| | http://www.unizh.ch/oci/group.pages/thiel/persons/turner/turner.html | ---------------------------------------------------------------------- - -- ______________________________________ Dr. Norman Goldberg (N.Goldberg@tu-bs.de) Technische Universitaet Braunschweig Institut fuer Organische Chemie Hagenring 30 D-38106 Braunschweig (FRG) Tel.: +(0)531-391-5312 Fax : +(0)531-391-5388 ______________________________________ --------------4048A47994E1F131C845CD56 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Here's the summary of the answers I obtained concerning the visualization
of G94 output under WIN95. Thanks to those who sent them!
-Norman

>Does someone out there know a convenient way to convert
>Gaussian output files (on unix machines) into decent publishable
>structures
>that can easily be modified (labelled, etc.) under Win95 and
>then imported into 'word'?

--------------------------------------.
I use Babel (free from the CCL archives) to convert more-or-less any common file
format, including Gaussian, to a sybyl mol2 file. I then ftp that >from the Unix
system to my Mac and read it directly into Chem3D. Chem3D provides numerous
annotation features and the resulting graphic can be directly imported into MS
Word. You could do exactly the same under Windows.

Hope this helps.

George

============================================================================
George P. Ford                      |     email:  gford@smu.edu
Department of Chemistry             |       web:  http://www.smu.edu/~gford/
Southern Methodist University       | telephone:  (214)768-2479
Dallas, Texas 75275                 |       fax:  (214)768-4089
============================================================================
 
Try the Molden program obtainable from:

http://www.caos.kun.nl/~schaft/molden/molden.html

>From the freeware programs I've come across this is the best, but if you do
come across any others more suitable for importing graphics into Windows
applications, I'd  appreciate the details.

Best regards,
Phil.

-------------------------------------------------------
Phil Branton.
Department of Chemistry,
University of Surrey,
Guildford, Surrey.  GU2 5XH.

Email:  p.branton@surrey.ac.uk
Tel:    +44 (0)1483 259591
FAX:    +44 (0)1483 259514
WWW:    http://www.surrey.ac.uk/~chp2pb/
-------------------------------------------------------

This is not all that straight forward - but it works.

Read the structure using Xmol and put out as XYZ.

Read into Rasmol and make look nice, export at BMP (or gif , then use XV
to make BMP).

Read into Microsoft Paint and lable + touch up on a pixel by pixel basis
(this works readly well).

Copy onto clipboard.

Past to Word.

Good luck

Alex
--

 ----------------------------------------------------------------------
| Dr. Alexander J Turner       |                                       |
| Universitaet Zuerich         |Tel.:    (41)-1-6354239                |
| Organisch-Chemisches Institut|Fax:     (41)-1-6356812                |
| Winterthurerstrasse 190      |                                       |
| CH-8057 Zuerich              |E-Mail:  turner@ocisgi28.unizh.ch      |
| Switzerland                  |                                       |
|----------------------------------------------------------------------|
| http://www.unizh.ch/oci/group.pages/thiel/persons/turner/turner.html |
 ----------------------------------------------------------------------
 
 
 
 

-

--
______________________________________

Dr. Norman Goldberg   (N.Goldberg@tu-bs.de)
Technische Universitaet Braunschweig
Institut fuer Organische Chemie
Hagenring 30
D-38106 Braunschweig (FRG)

Tel.: +(0)531-391-5312
Fax : +(0)531-391-5388
______________________________________
  --------------4048A47994E1F131C845CD56-- From schiffer@h1tw0036.hoechst.com Fri Jan 9 08:13:55 1998 Received: from www.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id IAA05156; Fri, 9 Jan 1998 08:12:00 -0500 (EST) Received: by www.hoechst.com id OAA11559; Fri, 9 Jan 1998 14:12:33 +0100 Received: from unknown(134.81.76.36) by www id sma011543; Fri Jan 9 14:12:18 1998 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA08204; Fri, 9 Jan 1998 14:05:56 +0100 Message-ID: <34B620B4.167E@h1tw0036.hoechst.com> Date: Fri, 09 Jan 1998 14:05:56 +0100 From: "Dr. Heinz Schiffer" Organization: Hoechst Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List Subject: Free program for CCSD(T) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Status: RO Content-Length: 715 Dear colleagues, does anybody knows a program to perform single point energy calculations on the CCSD(T) level, which can be downloaded for free and which runs on IBM RS/6000 (AIX 4.1) or SG Indigo2 (IRIX 5.3) platforms ? It should be able to do UHF SCF calculations and the corresponding CCSD(T) calculations especially with user-defined basis sets. Any hint I would greatly appreciate. Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From toukie@zui.unizh.ch Fri Jan 9 10:13:55 1998 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id JAA05690; Fri, 9 Jan 1998 09:44:53 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA12819; Fri, 9 Jan 1998 15:44:40 +0100 Message-Id: <3.0.3.32.19980109154742.00688500@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Fri, 09 Jan 1998 15:47:42 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: RasWin question Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Status: RO Content-Length: 820 Dear Colleagues; I have a PDB file of a polypeptide with a bound ligand, and there is a hydrogen bond between the -OH hydrogen of this ligand and a neighbouring Asp residue of the polypeptide. Is there a way of getting RasWin 2.6 to display this H-bond? At the command prompt I've typed display hbonds yellow or set hbonds sidechain display hbonds yellow but the image on the screen doesn't change, i.e., no H-bonds show up. However, using a different PC equipped with WebLab 2.0 or HyperChem, I can see the H-bond in question. Please advise me of what I am doing wrong and what I must type on the command line(s) in order to visualise this H-bond using RasWin 2.6. Thanks in advance to all responders. S. Shapiro toukie@zui.unizh.ch From tcg@chem.unipune.ernet.in Sat Jan 10 00:14:03 1998 Received: from naveen.ncst.ernet.in for tcg@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id AAA09661; Sat, 10 Jan 1998 00:11:20 -0500 (EST) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with SMTP id TAA26845 for ; Fri, 9 Jan 1998 19:15:18 +0530 Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA30568; Fri, 9 Jan 1998 19:04:23 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id TAA03461; Fri, 9 Jan 1998 19:00:44 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id TAA02957; Fri, 9 Jan 1998 19:13:22 -0500 Date: Fri, 9 Jan 1998 19:13:22 -0500 From: tcg@chem.unipune.ernet.in (Students of Dr. S.R. Gadre) Message-Id: <199801100013.TAA02957@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: XII ICCCRE Status: RO Content-Length: 1061 To: CHEMISTRY@www.ccl.net Dear Sirs/Madams : The XII International Conference on Computers in Chemical Research and Education (ICCCRE) was held in Pune University from Jan 5th to 9th of this year. The concluding session was held on 9th Jan >from 2:30 to 3:00 P.M. The Book of Abstracts, containing 120 abstracts of talks and posters presented in the conference, is available for a nominal price of U.S. dollars $50 plus handling charges. The talks fall under the following sessions: Quantum Chemical Methods. Computers in Chemical Education, Interfacing and Networking. Molecular Modelling, Simulations and Dynamics. New Methods and Algorithms, Artificial Intelligence, Neural Networks etc. Apart from this 67 posters were also presented in the conference. If anyone is interested in getting this book contact Prof. S.R. Gadre at gadre@chem.unipune.ernet.in or gadre@unipune.ernet.in. Thanks. Shridhar R. Gadre Convenor, XII ICCCRE