From dok707@cvx12.inet.dkfz-heidelberg.de Fri Feb 4 03:47:04 1994 Received: from cvx12.inet.dkfz-heidelberg.de for dok707@cvx12.inet.dkfz-heidelberg.de by www.ccl.net (8.6.4/930601.1506) id DAA23075; Fri, 4 Feb 1994 03:29:25 -0500 Received: by cvx12.inet.dkfz-heidelberg.de id AA19277 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Thu, 3 Feb 1994 14:44:22 +0100 Date: Thu, 3 Feb 1994 14:44:22 +0100 From: Frank Herrmann Message-Id: <199402031344.AA19277@cvx12.inet.dkfz-heidelberg.de> To: chemistry@ccl.net Subject: conformation generation from internal coordinates Hello, is there a program, that generates conformations from distances, angles and dihedrals if they are not given as a complete Z-Matrix (e.g. mopac input) ? It should use additional angles instead of missed dihedrals and detect or handle incomplete determination of the conformation. My actual problem is a conformation described in an article using only distances and angles and I want to generate either a PDB or a MOPAC input file. I guess the given values are not sufficient to determine the conformation. Any suggestions would be appreciated Thank you -------------------------------------------------- Frank Herrmann, Dept. of Molecular Biophysics 0810 German Cancer Research Center Im Neuenheimer Feld 280, D-69120 Heidelberg Tel: (49) 6221-422336, FAX: (49) 6221-422333 email: F.Herrmann@dkfz-heidelberg.de From brock@chemie.uni-hamburg.de Fri Feb 4 08:47:23 1994 Received: from deneb.dfn.de for brock@chemie.uni-hamburg.de by www.ccl.net (8.6.4/930601.1506) id IAA24433; Fri, 4 Feb 1994 08:17:45 -0500 Received: from fbihh.informatik.uni-hamburg.de by deneb.dfn.de (4.1/SMI-4.2) id AA27597; Fri, 4 Feb 94 14:17:12 +0100 Received: from [134.100.212.3] by fbihh.informatik.uni-hamburg.de (5.65+/FBIHH-1.29) with SMTP; id AA05289; Fri, 4 Feb 94 14:17:14 +0100 Received: by pcaix3.chemie.uni-hamburg.de (AIX 3.2/UCB 5.64/4.50) id AA08658; Fri, 4 Feb 1994 14:02:55 +0100 From: brock@chemie.uni-hamburg.de (Mathias Brock) Message-Id: <9402041302.AA08658@pcaix3.chemie.uni-hamburg.de> Subject: MOPAC93 alkali metal parametrization To: chemistry@ccl.net Date: Fri, 4 Feb 1994 14:02:55 +0100 (MEZ) Cc: brock@chemie.uni-hamburg.de (Mathias Brock) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 667 Dear netters, sorry for the last empty message (a bug caused by our elm-system). I hope your attention will still be existing today. My last question was: Does anybody know about papers dealing with MOPAC-parametrisation of alkaline, earth-alkaline (or transition) metals (ions or pure metals), which are not yet included in MOPAC93 ? In history of semiempirical calculation the right representation of ions (mostly electrostatic behaviour) was oversimplified. In some case these ions were reduced to point charges, on the other hand much too high charge transfer towards the ions was calculated. Thank you in advance. Mathias Brock brock@chemie.uni-hamburg.de From vkitzing@sunny.mpimf-Heidelberg.mpg.de Fri Feb 4 08:51:30 1994 Received: from foxy.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-Heidelberg.mpg.de by www.ccl.net (8.6.4/930601.1506) id IAA24453; Fri, 4 Feb 1994 08:29:26 -0500 Received: from sunny.mpimf-heidelberg.mpg.de by foxy.mpimf-heidelberg.mpg.de (5.65+/1.34) id AA19493; Fri, 4 Feb 94 14:26:58 +0100 Received: from [192.109.43.34] (mac10) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA19034; Fri, 4 Feb 94 14:25:25 +0100 Date: Fri, 4 Feb 94 14:25:25 +0100 Message-Id: <9402041325.AA19034@sunny.mpimf-Heidelberg.mpg.de> To: Frank Herrmann From: vkitzing@sunny.mpimf-Heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:conformation generation from internal coordinates Cc: chemistry@ccl.net >Hello, > >is there a program, that generates conformations from distances, >angles and dihedrals if they are not given as a complete Z-Matrix >(e.g. mopac input) ? It should use additional angles instead of missed >dihedrals and detect or handle incomplete determination of the >conformation. > >My actual problem is a conformation described in an article using only >distances and angles and I want to generate either a PDB or a MOPAC >input file. I guess the given values are not sufficient to determine >the conformation. Perhaps you can transform the given angles into distances. A distance geometry program may derive the space of consistent structures from this set of distances. ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizische Forschung Jahnstr. 29, D69120 Heidelberg, FRG FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de From davide@stinch0.csmtbo.mi.cnr.it Fri Feb 4 10:47:47 1994 Received: from stinch0.csmtbo.mi.cnr.it for davide@stinch0.csmtbo.mi.cnr.it by www.ccl.net (8.6.4/930601.1506) id KAA25290; Fri, 4 Feb 1994 10:11:29 -0500 From: Received: by stinch0.csmtbo.mi.cnr.it (911016.SGI/911001.SGI) for chemistry@ccl.net id AA28750; Fri, 4 Feb 94 16:10:40 +0100 Date: Fri, 4 Feb 94 16:10:40 +0100 Message-Id: <9402041510.AA28750@stinch0.csmtbo.mi.cnr.it> To: chemistry@ccl.net Subject: fourier-bessel transformation Hi, I would like some information about routines for Fourier-Bessel Transformation. any help? Thank you regards davide ------------------------------------------------------------------- Davide M. Proserpio - Istituto di Chimica Strutturistica Inorganica Universita' di Milano, Via Venezian, 21 - 20133 Milano, Italy phone +39-2-70635120 fax 70635288 - davide@stinch0.csmtbo.mi.cnr.it ------------------------------------------------------------------- From h.rzepa@ic.ac.uk Fri Feb 4 10:53:21 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id KAA25572; Fri, 4 Feb 1994 10:44:00 -0500 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <18320-0@punch.ic.ac.uk>; Fri, 4 Feb 1994 15:40:47 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA14506; Fri, 4 Feb 94 15:43:22 GMT Message-Id: <9402041543.AA14506@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 4 Feb 1994 15:43:42 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: CCL:MOPAC93 alkali metal parametrization >Dear netters, > >sorry for the last empty message (a bug caused by our elm-system). >I hope your attention will still be existing today. > >My last question was: >Does anybody know about papers dealing with MOPAC-parametrisation of >alkaline, earth-alkaline (or transition) metals (ions or pure metals), >which are not yet included in MOPAC93 ? > >In history of semiempirical calculation the right representation of >ions (mostly electrostatic behaviour) was oversimplified. In some case >these ions were reduced to point charges, on the other hand much too high >charge transfer towards the ions was calculated. > >Thank you in advance. > >Mathias Brock >brock@chemie.uni-hamburg.de > We have a paper about to appear in the March issue of Perkin Trans 2 (see http://www.ch.ic.ac.uk/rzepa/RSC/P2/3_07186C.html) dealing with those monovalent ions currently parameterised in MNDO, and PM3 (ie Li, Na, K, Ga etc) and comparing with LAN1DZ/ECP ab initio calculations. Basically, Na, K and Ga appear to have significant problems with energies if not with geometries. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.01, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From nmdl@rlmtc.DNET.hcc.com Fri Feb 4 13:47:13 1994 Received: from gatekeeper.hcc.com for nmdl@rlmtc.DNET.hcc.com by www.ccl.net (8.6.4/930601.1506) id MAA27276; Fri, 4 Feb 1994 12:53:35 -0500 From: Received: by gatekeeper.hcc.com (5.65/jj-092193); id AA09329; Fri, 4 Feb 94 12:53:34 -0500 Received: by mailgate.bridgewater.ne.hcc.com (5.65/ejc-092393< Who Loves Class M Planets>); id AA26162; Fri, 4 Feb 1994 12:53:28 -0500 Date: Fri, 4 Feb 1994 12:53:28 -0500 Message-Id: <9402041753.AA26162@mailgate.bridgewater.ne.hcc.com> To: "chemistry@ccl.net"@INET.DNET.hcc.com Subject: MNDO-D Greetings, Can anybody tell me about MNDO-d? Where is it available? Is there a parallel version. All the best, Sol Jacobson Hoechst Celanese From HUDECEK@prifuk.fns.uniba.sk Fri Feb 4 13:49:32 1994 Received: from eunet.EU.net for HUDECEK@prifuk.fns.uniba.sk by www.ccl.net (8.6.4/930601.1506) id NAA27412; Fri, 4 Feb 1994 13:06:13 -0500 Received: from sk2eu.eunet.sk (sk2eu.EUnet.sk [192.108.130.33]) by eunet.EU.net (8.6.4/8.6.4) with SMTP id TAA09890 for ; Fri, 4 Feb 1994 19:05:37 +0100 Received: from devin.fns.uniba.sk by sk2eu.eunet.sk with SMTP id AA07889 Fri, 4 Feb 1994 19:05:56 +0100 Received: from charon.fns.uniba.sk by devin.fns.uniba.sk (5.64/11.0) id AA25528; Fri, 4 Feb 94 19:04:46 +0100 Received: From PRIFUK/WORKQUEUE by charon.fns.uniba.sk via Charon 3.4 with IPX id 100.940204190619.256; 04 Feb 94 19:06:30 +0100 Message-Id: To: CHEMISTRY@ccl.net From: HUDECEK@fns.uniba.sk Date: 4 Feb 94 19:06:09 Subject: MOLGEN program available Priority: normal X-Mailer: Pegasus Mail v2.3 (R4). X-Charset: ASCII X-Char-Esc: 29 Dear Netters I placed a demo version of MOLGEN program in the CCL archives. MOLGEN is a powerful molecular graphics/chemical database/conformation analysis/fitting, etc. For more information consult the mg_demo.txt, and run the demo to see its capabilities. You can retrieve the program via anon.ftp/gopher from the directory pub/chemistry/chemistry/software/MOLGEN-demo or via e-mail by sending the following message: select chemistry limit 1.5MB size 60kB cd software/MOLGEN-demo ls get * quit to MAILSERV@ccl.net and files will be send to you in a uuencoded form. I invite your comments and hope to hear from you. Sincerely, Milan Hudecek, HUDECEK@fns.uniba.sk From marty@ionchannel.med.harvard.edu Fri Feb 4 13:50:01 1994 Received: from ionchannel.med.harvard.edu for marty@ionchannel.med.harvard.edu by www.ccl.net (8.6.4/930601.1506) id MAA27243; Fri, 4 Feb 1994 12:49:40 -0500 Received: by ionchannel.med.harvard.edu (931110.SGI/931108.SGI.AUTO.ANONFTP) for CHEMISTRY@oscsunb.ccl.net id AA14007; Fri, 4 Feb 94 10:10:22 -0800 Date: Fri, 4 Feb 94 10:10:22 -0800 From: marty@ionchannel.med.harvard.edu (Marty Gallagher) Message-Id: <9402041810.AA14007@ionchannel.med.harvard.edu> To: CHEMISTRY@oscsunb.ccl.net Subject: rational drug design Hello, A while back someone asked about success stories in rational drug design. In that light, what does the group think of the Merck groups article in *Science* 23:380-384 where they rationally designed inhibitors of HIV protease? -- Marty ======================================================================== Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave Boston, MA 02115 Neither Schrodinger nor Einstein "suberted the dominant paradigm." Rather, they complemented it in order to descibe areas of the Ultimate Reality that Newton did not see. Those who categorically reject tradition in order to avoid conformity are still bound by it. Those who seek truth for truth's sake are truly free. -- Me From HUDECEK@prifuk.fns.uniba.sk Fri Feb 4 15:49:39 1994 Received: from eunet.EU.net for HUDECEK@prifuk.fns.uniba.sk by www.ccl.net (8.6.4/930601.1506) id PAA28656; Fri, 4 Feb 1994 15:09:52 -0500 Received: from sk2eu.eunet.sk (sk2eu.EUnet.sk [192.108.130.33]) by eunet.EU.net (8.6.4/8.6.4) with SMTP id VAA12208 for ; Fri, 4 Feb 1994 21:09:36 +0100 Received: from devin.fns.uniba.sk by sk2eu.eunet.sk with SMTP id AA09371 Fri, 4 Feb 1994 21:10:09 +0100 Received: from charon.fns.uniba.sk by devin.fns.uniba.sk (5.64/11.0) id AA26017; Fri, 4 Feb 94 21:08:58 +0100 Received: From PRIFUK/WORKQUEUE by charon.fns.uniba.sk via Charon 3.4 with IPX id 100.940204211031.352; 04 Feb 94 21:10:42 +0100 Message-Id: To: CHEMISTRY@ccl.net From: HUDECEK@fns.uniba.sk Date: 4 Feb 94 21:10:23 Subject: MOLGEN - one more info, pardon me Priority: normal X-Mailer: Pegasus Mail v2.3 (R4). X-Charset: ASCII X-Char-Esc: 29 Excuse me, please, I forgot to mention that MOLGEN is for PC with DOS. Milan From jkshin@radon.sait.samsung.co.kr Fri Feb 4 21:49:44 1994 Received: from han.hana.nm.kr for jkshin@radon.sait.samsung.co.kr by www.ccl.net (8.6.4/930601.1506) id VAA02161; Fri, 4 Feb 1994 21:14:50 -0500 Received: from (saitgw.sait.samsung.co.kr) by han.hana.nm.kr (4.1/KUM-0.1) id AA27902; Sat, 5 Feb 94 11:16:30 KST Received: from radon.sait.samsung.co.kr by (4.1/SMI-4.1) id AA24450; Sat, 5 Feb 94 11:16:06 KST Received: by radon.sait.samsung.co.kr (920330.SGI/920502.SGI.AUTO) for @saitgw.sait.samsung.co.kr:chemistry@ccl.net id AA03647; Sat, 5 Feb 94 11:17:03 +0900 Date: Sat, 5 Feb 94 11:17:03 +0900 From: jkshin@radon.sait.samsung.co.kr (Jaikwang Shin) Message-Id: <9402050217.AA03647@radon.sait.samsung.co.kr> To: chemistry@ccl.net Subject: MRS address? Dear Netters: I would like to know the contact point of Materials Research Society (MRS), USA. Does anyone know the address(preferably e-mail address) of MRS? Please reply me to jkshin@radon.sait.samsung.co.kr Thanks in advance Jai K. Shin From jkl@ccl.net Fri Feb 4 22:49:45 1994 Received: from hawkeye.ccl.net for jkl@ccl.net by www.ccl.net (8.6.4/930601.1506) id WAA02531; Fri, 4 Feb 1994 22:05:52 -0500 From: Jan Labanowski Received: from localhost for jkl@ccl.net by hawkeye.ccl.net (8.6.4/920428.1525) id WAA11947; Fri, 4 Feb 1994 22:05:53 -0500 Date: Fri, 4 Feb 1994 22:05:53 -0500 Message-Id: <199402050305.WAA11947@hawkeye.ccl.net> To: jkshin@radon.sait.samsung.co.kr Subject: Violation of list rules In-Reply-To: Mail from 'jkshin@radon.sait.samsung.co.kr (Jaikwang Shin)' dated: Sat, 5 Feb 94 11:17:03 +0900 Cc: jkl@ccl.net, chemistry@ccl.net Dear Netters, Yes, I send reminding messages to list offenders... Reminder: Before you post to chemistry@ccl.net please READ THE HELP FILE and adhere strictly to the RULES of the list described thereof. You get the help file by sending: HELP CHEMISTRY to the address MAILSERV@ccl.net Some topic like: What is the address... Looking for a job... Position available... You dummy.... We sell good software cheap... are explicitly discouraged. I (jkl@ccl.net) am trying to handle them off-line, so please contact me before you get hate mail. Beware, many users treat policing the offenders of the list seriously (THANK YOU!!!) and you may feel very guilty after you commit your sin. Jan Labanowski Your coordinator jkl@ccl.net