From chemistry-request@server.ccl.net Mon Jun 7 02:33:44 1999 Received: from nic.upatras.gr (nic.upatras.gr [150.140.1.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA24625 for ; Mon, 7 Jun 1999 02:33:40 -0400 Received: (qmail 6018 invoked from network); 7 Jun 1999 06:27:08 -0000 Received: from titanas.chemistry.upatras.gr (150.140.180.134) by nic.upatras.gr with SMTP; 7 Jun 1999 06:27:08 -0000 Received: (qmail 1209 invoked from network); 7 Jun 1999 06:07:54 -0000 Received: from rea.chemistry.upatras.gr (HELO titanas.chemistry.upatras.gr) (150.140.180.157) by titanas.chemistry.upatras.gr with SMTP; 7 Jun 1999 06:07:54 -0000 Message-ID: <375B6AA8.69C3A84@titanas.chemistry.upatras.gr> Date: Mon, 07 Jun 1999 09:46:00 +0300 From: Demetrios Xenides X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: built G94W on a Linux (i686) Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 7bit Hi outhere, I tried to built the G94W source on a i686 machine running Linux (REDHAT5.1). Unfortunately the trial failed.... The bldg94.log ends up with the following: g94root:undefined variable Any help will be very much appreciated!!!!! Cheers email: qc2@chemistry.upatras.gr From chemistry-request@server.ccl.net Mon Jun 7 05:49:26 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA26417 for ; Mon, 7 Jun 1999 05:49:25 -0400 Received: from felix.orc.univie.ac.at (felix.orc.univie.ac.at [131.130.16.42]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id FAA27887 for ; Mon, 7 Jun 1999 05:43:33 -0400 (EDT) Received: (from wr@localhost) by felix.orc.univie.ac.at (8.9.1/8.9.1) id LAA09296 for chemistry@ccl.net; Mon, 7 Jun 1999 11:43:30 +0200 (MDT) From: "Robien Wolfgang" Message-Id: <9906071143.ZM9294@felix.orc.univie.ac.at> Date: Mon, 7 Jun 1999 11:43:30 -0600 To: chemistry@ccl.net X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) Subject: New_email_fax_and_phone Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19906071143.ZM9294.orc.univie.ac.at" --PART-BOUNDARY=.19906071143.ZM9294.orc.univie.ac.at X-Zm-Content-Name: info_file Content-Type: text/plain ; name="info_file" ; charset=us-ascii Dear Colleague; I would like to inform you about some changes of my personal coordinates: Ao. Univ. Prof. Dr. Wolfgang Robien Institute for Organic Chemistry University of Vienna Waehringerstr. 38, A-1090 Wien/Austria New email: wr@felix.orc.univie.ac.at (My old email-address will be closed on June 18th, 1999 / The CSEARCH-server running under "server@felix.orc.univie.ac.at" is not influenced by the changes mentioned above !) New phone: ++ 43 - 1 - 4277 - 52119 (valid: July 19th,1999 - ???? ) New fax: ++ 43 - 1 - 4277 - 52129 (valid: July 19th,1999 - ???? ) home - page: http://felix.orc.univie.ac.at/~wr/wr_pers.html Yours sincerely, Wolfgang Robien Note: A separate email-address for confidential messages is available upon request. --PART-BOUNDARY=.19906071143.ZM9294.orc.univie.ac.at-- From chemistry-request@server.ccl.net Mon Jun 7 16:07:06 1999 Received: from mb05.swip.net (mb05.swip.net [193.12.122.209]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA03530 for ; Mon, 7 Jun 1999 16:07:05 -0400 Received: from default (dialup152-2-20.swipnet.se [130.244.152.84]) by mb05.swip.net (8.8.8/8.8.8) with SMTP id WAA20108 for ; Mon, 7 Jun 1999 22:01:06 +0200 (MET DST) Message-ID: <00ff01beb120$850dda60$9128f482@default> From: "=?iso-8859-1?Q?=D6BERG_TOMAS?=" To: Subject: Electronic reprint of textbook on optimization in chemistry Date: Mon, 7 Jun 1999 22:01:10 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id QAA03531 The textbook "Sequential Simplex Optimization: A technique for Improving Quality and Productivity in Research, Development, and Manufacturing" by F. H. Walters et al has been out of print for some time. CRC Press LLC has now licensed us the right to make electronic reprints of this excellent text. We wish to continue the work to popularize the simplex methodology, and make it an everyday tool for many more professionals and researchers. We have therefore decided to publish and distribute the electronic reprint through our web site. You may freely browse the whole text as HTML or download it as an Adobe Acrobat PDF-file from http://www.multisimplex.com Best regards, Tomas Oberg MultiSimplex AB tomas.oberg@multisimplex.com From chemistry-request@server.ccl.net Mon Jun 7 03:45:05 1999 Received: from email.guomai.sh.cn (qwajtuimzw@e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA25166 for ; Mon, 7 Jun 1999 03:45:04 -0400 Received: from guomai.sh.cn (13-114.guomai.sh.cn) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.01.13.19.49.p4) with ESMTP id <0FCY001KB5C88J@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Mon, 7 Jun 1999 15:40:57 +0800 (CST) Date: Mon, 07 Jun 1999 15:36:58 +0800 From: Yubo Fan Subject: How to convert eu into Kcal/mol/K To: CHEMISTRY@ccl.net Message-id: <375B7698.5C2BE046@guomai.sh.cn> Organization: Fudan University MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (Win98; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear CCLers, I met a rather old unit (eu) using to entropy. How can I convert it into IS unit? Could you please tell me the conversion factor. With best regards Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Mon Jun 7 09:27:57 1999 Received: from stark.udg.es (stark.udg.es [130.206.128.61]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA31594 for ; Mon, 7 Jun 1999 09:27:10 -0400 Received: (from xavier@localhost) by stark.udg.es (950413.SGI.8.6.12/950213.SGI.AUTOCF) id OAA03020 for chemistry@ccl.net; Mon, 7 Jun 1999 14:29:54 -0200 Date: Mon, 7 Jun 1999 14:29:54 -0200 From: xavier@stark.udg.es (Xavier Fradera) Message-Id: <199906071629.OAA03020@stark.udg.es> Apparently-To: chemistry@ccl.net Hi, a few days ago, I asked for a program that could convert sybyl atom types to MM2 or other force- fields for use in tinker. A. Stevens and C. Gonzalez suggested using the Babel program. I have tried babel-1.6. It can read sybyl mol2 fields and write MM2, MM3 and tinker input files, among other. However, I am not absolutely sure that the atom type conversion is done adequately. For instance, I have tried translating a mol2 file for a small molecule (benz.mol2) to a tinker file (benz.xyz) (files are at the end) The atom types generated for a tinker output coincide with those generated for MM2 and MM3, so i tried running tinker single-point energy calculations using the MM2, MM3 and tinker parameter sets. In all cases, tinker fails to calculate the energy because it finds bonds (and torsions) for which it has no parameters, e.g., for the MM2 force-field: Undefined Bond Stretching Parameters : Type Atom Names Atom Classes Bond 1-C 7-C+ 2 30 Bond 7-C+ 8-N 30 9 Bond 7-C+ 9-N 30 9 Bond 8-N 15-H 9 23 etc. It happens the same for most of the molecules I have tried. Anyone has had similar problems ? Is this actually a problem in the atom type translation or rather a limitation of the MM2 force-field ? (this molecule is actually [(C6H6)-C-(NH2)2]+) Thanks. -- Xavier Fradera ------------ (benz.mol2) @MOLECULE bezamidine 18 18 1 0 1 PROTEIN GASTEIGER INVALID_CHARGES @DICT PROTEIN protein @ATOM 1 C1 6.2540 17.3460 23.1660 C.ar 1 BENZ1 0.0932 2 C2 5.9180 16.1210 22.5890 C.ar 1 BENZ1 -0.0269 3 C3 4.7620 16.0230 21.7990 C.ar 1 BENZ1 -0.0523 4 C4 3.9480 17.1560 21.6060 C.ar 1 BENZ1 -0.0554 5 C5 4.3030 18.3840 22.1750 C.ar 1 BENZ1 -0.0523 6 C6 5.4510 18.4930 22.9710 C.ar 1 BENZ1 -0.0269 7 C7 7.4670 17.4620 23.9910 C.cat 1 BENZ1 0.2620 8 N8 8.2990 16.3920 24.2200 N.pl3 1 BENZ1 -0.2466 9 N9 7.8230 18.6310 24.5880 N.pl3 1 BENZ1 -0.2466 10 H10 6.5450 15.2514 22.7496 H 1 BENZ1 0.0693 11 H11 4.4965 15.0781 21.3388 H 1 BENZ1 0.0653 12 H12 3.0431 17.0764 21.0145 H 1 BENZ1 0.0649 13 H13 3.6855 19.2573 21.9988 H 1 BENZ1 0.0653 14 H14 5.7182 19.4387 23.4285 H 1 BENZ1 0.0693 15 H15 9.1401 16.5092 24.8028 H 1 BENZ1 0.2545 16 H16 8.0813 15.4731 23.8088 H 1 BENZ1 0.2545 17 H17 7.2438 19.4728 24.4583 H 1 BENZ1 0.2545 18 H18 8.6718 18.6745 25.1698 H 1 BENZ1 0.2545 @BOND 1 1 2 ar 2 1 6 ar 3 1 7 1 4 2 3 ar 5 2 10 1 6 3 4 ar 7 3 11 1 8 4 5 ar 9 4 12 1 10 6 5 ar 11 5 13 1 12 6 14 1 13 7 8 1 14 7 9 1 15 8 15 1 16 8 16 1 17 9 17 1 18 9 18 1 @SUBSTRUCTURE 1 BENZ1 9 RESIDUE 1 I **** 0 ROOT @SET UNK_ATOMS STATIC ATOMS AMSOM **** Atom types guessed for these atoms 9 1 2 3 4 5 6 7 8 9 ------------ (benz.xyz) 18 bezamidine 1 C 6.254000 17.346000 23.166000 2 2 6 7 2 C 5.918000 16.121000 22.589000 2 1 3 10 3 C 4.762000 16.023000 21.799000 2 2 4 11 4 C 3.948000 17.156000 21.606000 2 3 5 12 5 C 4.303000 18.384000 22.175000 2 4 6 13 6 C 5.451000 18.493000 22.971000 2 1 5 14 7 C 7.467000 17.462000 23.991000 30 1 8 9 8 N 8.299000 16.392000 24.220000 9 7 15 16 9 N 7.823000 18.631000 24.588000 9 7 17 18 10 H 6.545000 15.251400 22.749600 5 2 11 H 4.496500 15.078100 21.338800 5 3 12 H 3.043100 17.076400 21.014500 5 4 13 H 3.685500 19.257300 21.998800 5 5 14 H 5.718200 19.438700 23.428500 5 6 15 H 9.140100 16.509200 24.802800 23 8 16 H 8.081300 15.473100 23.808800 23 8 17 H 7.243800 19.472800 24.458300 23 9 18 H 8.671800 18.674500 25.169800 23 9