From chemistry-request@ccl.net Thu Mar 11 10:40:02 2004 Received: from mr2.cc.ic.ac.uk (mr2.cc.ic.ac.uk [155.198.5.112]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2BFe1js016069 for ; Thu, 11 Mar 2004 10:40:01 -0500 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by mr2.cc.ic.ac.uk with esmtp (Exim 3.36 #1) id 1B1SJr-0001gi-02; Thu, 11 Mar 2004 15:41:59 +0000 Received: from rzepa-mac.ch.ic.ac.uk ([155.198.234.86]) by chcmga.ch.ic.ac.uk with esmtp (Exim 3.36 #1) id 1B1SL7-007bUS-00; Thu, 11 Mar 2004 15:43:17 +0000 Mime-Version: 1.0 X-Sender: rzepa=at=argon.ch.ic.ac.uk Message-Id: Date: Thu, 11 Mar 2004 15:41:54 +0000 To: chemweb=at=imperial.ac.uk, chemistry=at=ccl.net From: "Rzepa, Henry" Subject: CMLRSS: A Peer to Peer Chemical Information System Content-Type: text/plain; charset="us-ascii" X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net As part of a session on "Research Collaboratories, Virtual laboratories and Grid Computing" at the forthcoming ACS meeting (http://oasys2.confex.com/acs/227nm/techprogram/ ) we are presenting on "Semantic Grid computing - the WorldWideMolecularMatrix" Part of this will focus on the theme of RSS which I posted about last year. We have now developed a chemical component to this, now christened CMLRSS, and it is the purpose of this email to invite people if they wish, to join in to this "virtual laboratory", and hence "participate" in the ACS session. The procedure is as follows a) For an introduction to the concept, see eg http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/ or http://wwmm.ch.cam.ac.uk/moin/CmlRss b)We have prepared a distribution kit available either from http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/ or from http://wwmm.ch.cam.ac.uk/moin/RssClient We emphasize that whilst we believe this to function correctly, it has not yet been comprehensively tested on all platforms, and some components are still at the "late alpha", or "early beta" stage. Needless to say, we welcome comments and reports of bugs! c) You can view the existing CMLRSS grid by installing either Jmol (a 3D molecule viewer) or JChempaint (a 2D editor) as provided, along with the CMLRSS plugin in the kit (these are Java programs so you will have to have Java installed). By running this, you will open around 8 existing RSS "Channels" and hence subscribe to chemical feeds from these sites. You can if you wish aggregate these feeds into one, then filter them down by (e.g. element). You will notice several themes in the existing channels, including an aggregation of the long running "Molecules of the Month" sites, several database sites (NMR, X-Ray, ChemStock) and the World-Wide Molecular Matrix. d) You are also welcome to follow the instructions in the above distribution to create your own CMLRSS channel (I might add that several of the sites mentioned above were our beta testers for this kit; it took only one or two days to get up and running). If you do so, please let us know so that we can add you to the list (one of the many "todo" items is to organise the addition of further channels in a better way). I should end with the observation that as far as we know, this is the furthest that the RSS concept has been pushed into a science field, and another step towards the "semantic web" espoused by Sir Tim Berners-Lee. We would of course love to hear about your experiences with this system. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From chemistry-request@ccl.net Wed Mar 10 20:07:07 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2B174js006981 for ; Wed, 10 Mar 2004 20:07:04 -0500 Received: from cornell.edu (67-41-169-107.slkc.qwest.net [67.41.169.107]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i2B18o8t001565; Wed, 10 Mar 2004 20:09:05 -0500 (EST) Message-ID: <404FBC21.3040203(at)cornell.edu> Date: Wed, 10 Mar 2004 18:08:49 -0700 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry(at)ccl.net" Subject: Anti-bacterial database? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-PMX-Version: 4.5.0.92886, Antispam-Core: 4.0.4.92622, Antispam-Data: 2004.3.10.93953 X-Spam-Status: No, hits=0.9 required=7.0 tests=FROM_ENDS_IN_NUMS, TO_ADDRESS_EQ_REAL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all Does anyone know where I can find a database of anti-bacterial compounds, hopefully in SDF format and maybe free of charge? Thanks in advance, Richard -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 From chemistry-request@ccl.net Thu Mar 11 06:44:17 2004 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2BBiEjs020558 for ; Thu, 11 Mar 2004 06:44:15 -0500 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id TAA01727 for ; Thu, 11 Mar 2004 19:42:20 +0800 Message-Id: <200403111142.TAA01727*at*mx1.ustc.edu.cn> Date: Thu, 11 Mar 2004 19:44:22 +0800 From: "6!Q8@W" Reply-To: dxl*at*mail.ustc.edu.cn To: CCL Subject: vibrational scaling factor for PW91PW91 Organization: VP9z?F4sQ!<|;/Q'J5QiJR X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" X-Spam-Status: No, hits=4.3 required=7.0 tests=HEAD_ILLEGAL_CHARS autolearn=no version=2.61 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2BBiHjs020578 Dear CCLer#: !!!!Where can I find the vibrational scaling factor for PW91PW91/6-311+G(3df) ? Thank you for your help!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!Ding Xunlei !!!!!!!!!!!!!!!!!!!!!!!!!!!!2004-03-11 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl*at*mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl From chemistry-request@ccl.net Thu Mar 11 16:27:42 2004 Received: from mxout3.cac.washington.edu (mxout3.cac.washington.edu [140.142.32.166]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2BLRejs029552 for ; Thu, 11 Mar 2004 16:27:41 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout3.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.02) with ESMTP id i2BLTjHm030126 for ; Thu, 11 Mar 2004 13:29:45 -0800 Received: from u.washington.edu (D-128-95-235-225.dhcp4.washington.edu [128.95.235.225]) (authenticated bits=0) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.02) with ESMTP id i2BLTiaR028333 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 11 Mar 2004 13:29:44 -0800 Message-ID: <4050DA4E.2060300=at=u.washington.edu> Date: Thu, 11 Mar 2004 13:29:50 -0800 From: Oliver Hucke User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL Subject: CCL: MOE - MMFF94s geometry and 9-6 van der Waals potential Content-Type: multipart/mixed; boundary="------------020202020400050905000107" X-Spam-Status: No, hits=0.0 required=7.0 tests=LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --------------020202020400050905000107 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear All, I am using the program MOE to address a ligand docking problem. During this work the following questions arose: 1. With the MMFF94s force field some of my small molecules show strange geometries if I use force field charges. An example is the 4-cyano-anilin attached to this email. The aromatic ring is not really planar and the substituents are far from being in plane of the ring!? The problem seems to occur upon presence of the nitrogen. With MMFF94 I obtain the same result. Has somebody an explanation for the strange geometry obtained after MMFF94(s) energy minimization? 2. I would like to use a 9-6 van der Waals potential. I figured out that I need to adjust the parameters "Buffer1" and "Buffer2" in the potential setup. Which values would I have to assign? Your help is very much appreciated. Best regards, Oliver -- _______________________________________________________________ Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ohucke=at=u.washington.edu _______________________________________________________________ --------------020202020400050905000107 Content-Type: text/plain; name="mmff_problem.pdb" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="mmff_problem.pdb" HETATM 1 C8 SCH 2002 106.876 19.189 33.807 0.00 C HETATM 2 H SCH 2002 107.539 18.490 34.313 0.00 H HETATM 3 C13 SCH 2002 106.222 18.802 32.656 0.00 C HETATM 4 H SCH 2002 106.376 17.804 32.256 0.00 H HETATM 5 C15 SCH 2002 105.415 19.716 31.980 0.00 C HETATM 6 N2 SCH 2002 104.998 19.411 30.700 0.00 N HETATM 7 H SCH 2002 104.152 19.917 30.398 0.00 H HETATM 8 H SCH 2002 104.806 18.410 30.544 0.00 H HETATM 9 C9 SCH 2002 105.259 21.022 32.441 0.00 C HETATM 10 H SCH 2002 104.669 21.737 31.876 0.00 H HETATM 11 C10 SCH 2002 105.907 21.423 33.591 0.00 C HETATM 12 H SCH 2002 105.818 22.453 33.930 0.00 H HETATM 13 C11 SCH 2002 106.733 20.506 34.236 0.00 C HETATM 14 C SCH 2002 107.564 20.967 35.270 0.00 C HETATM 15 N SCH 2002 108.323 21.370 36.038 0.00 N CONECT 1 2 3 13 CONECT 2 1 CONECT 3 1 4 5 CONECT 4 3 CONECT 5 3 6 9 CONECT 6 5 7 8 CONECT 7 6 CONECT 8 6 CONECT 9 5 10 11 CONECT 10 9 CONECT 11 9 12 13 CONECT 12 11 CONECT 13 1 11 14 CONECT 14 13 15 CONECT 15 14 END --------------020202020400050905000107-- From chemistry-request@ccl.net Thu Mar 11 13:50:58 2004 Received: from 02-csexch.uopnet.plymouth.ac.uk (ils111.uopnet.plymouth.ac.uk [141.163.66.73]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2BIovjs023385 for ; Thu, 11 Mar 2004 13:50:58 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Disposition-Notification-To: "C Anthony Lewis" Subject: RE: [chemweb] CMLRSS: A Peer to Peer Chemical Information System Date: Thu, 11 Mar 2004 18:52:38 -0000 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [chemweb] CMLRSS: A Peer to Peer Chemical Information System Thread-Index: AcQHgD+FlnsaEAVzSrCEVADXPyP9fQAGOLoQ From: "C Anthony Lewis" To: "Rzepa, Henry" , , X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2BIowjs023389 Hello, This looks exciting... Not that really I understand what's going on! However, when I tried to run the RssClient Windows "Without Java VM" self extractor (from http://wwmm.ch.cam.ac.uk/moin/RssClient), I obtained an InstallAnywhere error saying the trial period had expired. Is this something I'm doing wrong? Anthony Lewis C. Anthony Lewis Petroleum & Environmental Geochemistry Group, School of Earth, Ocean and Environmental Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, U.K. tel: +44 (0)1752 233000 ext. 2988 FAX: +44 (0)1752 233035 e-mail: calewis(at)plymouth.ac.uk -----Original Message----- From: chemweb-bounces(at)imperial.ac.uk [mailto:chemweb-bounces(at)imperial.ac.uk] On Behalf Of Rzepa, Henry Sent: 11 March 2004 15:42 To: chemweb(at)imperial.ac.uk; chemistry(at)ccl.net Subject: [chemweb] CMLRSS: A Peer to Peer Chemical Information System As part of a session on "Research Collaboratories, Virtual laboratories and Grid Computing" at the forthcoming ACS meeting (http://oasys2.confex.com/acs/227nm/techprogram/ ) we are presenting on "Semantic Grid computing - the WorldWideMolecularMatrix" Part of this will focus on the theme of RSS which I posted about last year. We have now developed a chemical component to this, now christened CMLRSS, and it is the purpose of this email to invite people if they wish, to join in to this "virtual laboratory", and hence "participate" in the ACS session. The procedure is as follows a) For an introduction to the concept, see eg http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/ or http://wwmm.ch.cam.ac.uk/moin/CmlRss b)We have prepared a distribution kit available either from http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/ or from http://wwmm.ch.cam.ac.uk/moin/RssClient We emphasize that whilst we believe this to function correctly, it has not yet been comprehensively tested on all platforms, and some components are still at the "late alpha", or "early beta" stage. Needless to say, we welcome comments and reports of bugs! c) You can view the existing CMLRSS grid by installing either Jmol (a 3D molecule viewer) or JChempaint (a 2D editor) as provided, along with the CMLRSS plugin in the kit (these are Java programs so you will have to have Java installed). By running this, you will open around 8 existing RSS "Channels" and hence subscribe to chemical feeds from these sites. You can if you wish aggregate these feeds into one, then filter them down by (e.g. element). You will notice several themes in the existing channels, including an aggregation of the long running "Molecules of the Month" sites, several database sites (NMR, X-Ray, ChemStock) and the World-Wide Molecular Matrix. d) You are also welcome to follow the instructions in the above distribution to create your own CMLRSS channel (I might add that several of the sites mentioned above were our beta testers for this kit; it took only one or two days to get up and running). If you do so, please let us know so that we can add you to the list (one of the many "todo" items is to organise the addition of further channels in a better way). I should end with the observation that as far as we know, this is the furthest that the RSS concept has been pushed into a science field, and another step towards the "semantic web" espoused by Sir Tim Berners-Lee. We would of course love to hear about your experiences with this system. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). _______________________________________________ chemweb mailing list chemweb(at)imperial.ac.uk http://mailman.ic.ac.uk/mailman/listinfo/chemweb List coordinator, Henry Rzepa (mailto:rzepa(at)ic.ac.uk)