From chemistry-request@ccl.net Mon Jan 10 05:38:16 2005 Received: from stvsfimr002.ggr.co.uk (stvsfimr002.gsk.com [193.128.25.230]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0AAcEJB018064 for >ccl.net>; Mon, 10 Jan 2005 05:38:15 -0500 Received: from stvsasmtp04.ggr.co.uk ([147.184.2.62]) by stvsfimr002.ggr.co.uk with ESMTP id j0AAcjov022379 for >ccl.net>; Mon, 10 Jan 2005 10:38:49 GMT Received: from ukz1096.ggr.co.uk (ukz1096.ggr.co.uk [147.184.4.13]) by stvsasmtp04.ggr.co.uk (Switch-3.1.7/Switch-3.1.7) with ESMTP id j0AAsWpw024256 for >ccl.net>; Mon, 10 Jan 2005 10:55:27 GMT Received: from 147.184.2.6 by ukz1096.ggr.co.uk with ESMTP (Tumbleweed SMTP Relay); Mon, 10 Jan 2005 10:55:22 +0100 Received: from stvsnim001.sb.com (stvsnim001.sb.com [147.184.5.110]) by stvsasmtp01.ggr.co.uk (Switch-3.1.7/Switch-3.1.7) with ESMTP id j0AAtMPd017945 for >ccl.net>; Mon, 10 Jan 2005 10:55:22 GMT To: chemistry<>ccl.net Subject: UK QSAR and ChemoInformatics Spring Meeting MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0 September 26, 2002 Message-ID: >sb.com> From: iain.m.mclay<>gsk.com Date: Mon, 10 Jan 2005 10:53:54 +0000 X-MIMETrack: Serialize by Router on STVSNIM001/Servers/GSK(Release 5.0.10 |March 22, 2002) at 10/01/2005 10:55:22, Serialize complete at 10/01/2005 10:55:22 X-WSS-ID: 6DFC80907950143-01-01 Content-Type: multipart/alternative; boundary="=_alternative 003BFF5480256F85_=" X-Spam-Status: No, hits=7.2 required=7.5 tests=CLICK_BELOW,FVGT_m_MULTI_ODD2, FVGT_s_OBFU_Q1,HTML_MESSAGE,MK_BAD_HTML_04,NO_RDNS2,NO_REAL_NAME 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 multipart message in MIME format. --=_alternative 003BFF5480256F85_= Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit UK QSAR and Chemoinformatics Group is pleased to announce that registration is now being taken for the Spring 2005 meeting. The event will be hosted by IDBS and the University of Surrey and will take place on 13th and 14th April 2005 in Guildford. There is a great programme lined up, including talks > from Alex Tropsha, Joanna Jaworska, Peter Willett and Lowell Hall, as well as a technology afternoon at IDBS with workshops and a conference dinner. For full details of the event including how to register, click here: http://www.ukqsar2005.com/ The UK QSAR group meeting itself will be on the 14th April with an opportunity, on the 13th April, to learn more about IDBS's new Drug Discovery Technologies. As usual, posters will be an important part of the meeting, so please present your recent work to the rest of the Group (a check box for poster presentations is included on the online booking form). If you have any queries relating to the event please contact the organisers: Beth Thomas and Melanie Strangwick, IDBS +44 (0) 1483 595 010 ukqsar<>idbs.com http://www.idbs.com --=_alternative 003BFF5480256F85_= Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit
UK QSAR and Chemoinformatics Group is pleased to announce that registration is now
being taken for the Spring 2005 meeting. The event will be hosted by IDBS
and the University of Surrey and will take place on 13th and 14th April
2005 in Guildford. There is a great programme lined up, including talks
> from Alex Tropsha, Joanna Jaworska, Peter Willett and Lowell Hall, as well
as a technology afternoon at IDBS with workshops and a conference dinner.

For full details of the event including how to register, click here:
http://www.ukqsar2005.com/

The UK QSAR group meeting itself will be on the 14th April with an opportunity, on
the 13th April, to learn more about IDBS's new Drug Discovery Technologies.

As usual, posters will be an important part of the meeting, so please
present your recent work to the rest of the Group (a check box for poster
presentations is included on the online booking form).

If you have any queries relating to the event please contact the
organisers:

Beth Thomas and Melanie Strangwick, IDBS
+44 (0) 1483 595 010
ukqsar<>idbs.com
http://www.idbs.com

--=_alternative 003BFF5480256F85_=-- From chemistry-request@ccl.net Mon Jan 10 00:08:04 2005 Received: from mailhub1.uq.edu.au (mailhub1.uq.edu.au [130.102.148.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0A581o1005197 for ; Mon, 10 Jan 2005 00:08:02 -0500 Received: from smtp2.uq.edu.au (smtp2.uq.edu.au [130.102.5.53]) by mailhub1.uq.edu.au (8.12.11/8.12.11) with ESMTP id j0A5PHn7018092 for ; Mon, 10 Jan 2005 15:25:17 +1000 (EST) Received: from uq.edu.au (gonzo.soe.uq.edu.au [130.102.5.131]) by smtp2.uq.edu.au (8.12.10/8.12.10) with ESMTP id j0A5PHJh003068 for ; Mon, 10 Jan 2005 15:25:17 +1000 (EST) Received: from [152.98.207.35] by msg2b.soe.uq.edu.au (mshttpd); Mon, 10 Jan 2005 15:25:17 +1000 From: Dr Seth OLSEN To: chemistry(at)ccl.net Message-ID: Date: Mon, 10 Jan 2005 15:25:17 +1000 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) MIME-Version: 1.0 Content-Language: en Subject: CCL: GAMESS/TINKER IMOMM - $DATA needed? X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 on UQ Mailhub X-Spam-Status: No, hits=5.5 required=7.5 tests=IMPRONONCABLE_1, LINES_OF_YELLING,TRACKER_ID autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Collegues, I'm training myself on GAMESS/TINKER. The cyclopentene test jobs that are found in the documentation by Cheol Ho Choi run fine on my installation, so I have tried to work up my own input for a short peptide with a modified AA in the quantum region. When I attempt to run it, GAMESS terminates an error saying that no $DATA group was found. However, the documentation states that if all the coordinates are to be given in the $TINKEY field for an IMOMM job than no $DATA group should be necessary. Moreover, the cyclopentene IMOMM job with the commented-out $DATA field works fine. Can anyone tell me what is going wrong. My input deck follows: $CNTRL SCFTYP=RHF RUNTYP=optimize MULT=1 EXETYP=RUN COORD=TINKER ICHARGE=-1 NZVAR=288 $END $BASIS GBASIS=sto NGAUSS=3 $END $ZMAT DLC=.T. AUTO=.T. $END $TINXYZ 98 molden generated tinker .xyz (mm3 param.) 1 N 2.559668 2.032808 -3.447687 9 2 5 2 C 2.409374 0.791493 -3.995053 2 1 3 6 3 C 3.091461 -0.221384 -3.163879 2 2 4 14 4 N 3.643847 0.521384 -2.090885 9 3 5 15 5 C 3.282523 1.901012 -2.323878 2 1 4 18 6 C 1.674909 0.638310 -5.162475 1 2 7 72 7 C 1.390048 -0.427314 -6.208361 2 6 8 12 8 C 1.385198 -0.108612 -7.595450 2 7 9 73 9 C 1.123963 -1.102110 -8.579234 2 8 10 75 10 C 0.863466 -2.433252 -8.176489 2 9 11 13 11 C 0.861515 -2.784286 -6.799471 2 10 12 76 12 C 1.124320 -1.779122 -5.825405 2 7 11 74 13 O 0.608228 -3.385039 -9.132900 6 10 14 O 3.191780 -1.446907 -3.324064 6 3 15 C 4.467595 -0.119207 -0.937780 2 4 16 71 98 16 C 3.997365 -0.216336 0.142884 2 15 17 31 17 O 4.713328 -0.722068 1.136396 7 16 18 C 3.599556 3.065572 -1.539910 1 5 19 26 19 N 4.553110 3.025072 -0.702565 9 18 20 20 C 5.684243 3.302363 -0.108162 2 19 21 37 21 C 7.092847 3.591389 -0.572584 1 20 22 38 65 22 N 7.327498 2.960719 -1.867530 9 21 23 64 23 C 7.830224 1.735879 -1.980832 2 22 24 40 24 C 8.039690 1.226535 -3.412755 1 23 25 41 57 25 N 7.377170 2.101644 -4.392468 8 24 55 56 26 C 2.833227 4.364368 -1.768142 2 18 27 69 97 27 C 2.237451 5.011108 -0.507705 2 26 28 70 96 28 C 1.865011 6.456835 -0.576499 2 27 29 30 29 O 2.007205 7.101498 -1.621383 7 28 30 N 1.369226 7.017306 0.563699 9 28 77 78 31 N 2.735860 0.221656 0.296373 9 16 32 79 32 C 2.090153 0.180805 1.609199 1 31 33 35 80 33 C 0.705437 -0.446002 1.468128 2 32 34 46 34 O -0.328762 0.210937 1.636028 7 33 35 C 1.984037 1.604564 2.154295 1 32 36 81 82 36 O 1.383837 1.633184 3.440250 7 35 94 37 O 5.385773 3.315266 1.086135 7 20 38 C 7.277566 5.102506 -0.694850 1 21 39 66 67 39 S 8.922188 5.582399 -1.219971 15 38 68 40 O 8.108043 1.031231 -1.005976 7 23 41 C 9.548903 1.143626 -3.678073 1 24 42 58 59 42 C 9.970547 1.105082 -5.153271 1 41 43 60 61 43 C 9.094567 0.213307 -6.005771 2 42 44 45 44 O 8.540316 -0.781940 -5.528265 7 43 45 N 8.972657 0.560148 -7.288256 9 43 62 63 46 N 0.713449 -1.740104 1.180043 9 33 47 83 47 C -0.492284 -2.514811 0.933964 1 46 48 50 84 48 C -1.579338 -2.549761 2.016295 2 47 49 54 49 O -1.399392 -1.844427 3.212172 0 48 95 50 C -0.116283 -3.969867 0.558810 1 47 51 53 85 51 C 1.222349 -3.993314 -0.198492 1 50 52 86 87 52 C 1.241007 -3.165103 -1.480834 1 51 91 92 93 53 C -1.198101 -4.572065 -0.326708 1 50 88 89 90 54 O -2.609380 -3.198813 1.831173 7 48 55 H 6.707356 1.550632 -4.948018 5 25 56 H 6.876161 2.853334 -3.897643 5 25 57 H 7.586799 0.229924 -3.520723 5 24 58 H 10.020885 2.023145 -3.215816 5 41 59 H 9.873152 0.183037 -3.251307 5 41 60 H 9.923758 2.127612 -5.556067 5 42 61 H 10.988634 0.690100 -5.189157 5 42 62 H 9.444407 1.365605 -7.632806 5 45 63 H 8.409984 0.013364 -7.900181 5 45 64 H 7.103100 3.465759 -2.694940 5 22 65 H 7.810952 3.187315 0.156146 5 21 66 H 6.552723 5.483409 -1.429367 5 38 67 H 7.120716 5.529345 0.306753 5 38 68 H 9.824291 5.275534 -0.235621 5 39 69 H 2.298758 4.556666 -2.664884 5 26 70 H 2.362692 4.566933 0.448229 5 27 71 H 4.776843 -1.132347 -1.006291 5 15 72 H 1.129903 1.501971 -5.571202 5 6 73 H 1.580139 0.888958 -7.901449 5 8 74 H 1.122910 -2.038240 -4.796018 5 12 75 H 1.124432 -0.846417 -9.609479 5 9 76 H 0.666471 -3.783937 -6.500411 5 11 77 H 1.271088 6.466797 1.386701 5 30 78 H 1.105651 7.976720 0.572553 5 30 79 H 2.237332 0.576271 -0.488320 5 31 80 H 2.682543 -0.426594 2.309297 5 32 81 H 2.993677 2.035749 2.222904 5 35 82 H 1.351203 2.187002 1.468519 5 35 83 H 1.591181 -2.205999 1.129534 5 46 84 H -0.964629 -1.956780 0.112081 5 47 85 H -0.023795 -4.557660 1.483984 5 50 86 H 2.002968 -3.605035 0.472235 5 51 87 H 1.392521 -5.037675 -0.499077 5 51 88 H -1.677768 -5.411062 0.198654 5 53 89 H -1.951985 -3.804978 -0.557442 5 53 90 H -0.746205 -4.935411 -1.261464 5 53 91 H 0.738289 -3.722234 -2.285123 5 52 92 H 0.715894 -2.213683 -1.310363 5 52 93 H 2.282527 -2.962591 -1.771050 5 52 94 H 1.334402 2.531031 3.746726 0 36 95 H -2.157866 -1.968973 3.770477 0 49 96 H 1.160096 5.003379 -0.349066 20000 27 97 H 3.355150 5.319203 -1.725626 20000 26 98 H 5.354551 0.511009 -0.892414 20000 15 $END $LINK IMOMM=.T. IQMATM=20,37,19,18,5,1,2,3,4,15,71,98,14,6,72,7,12,74,11,76,10,13,9,75,8,73 LINKGE=15,16, 20,21, 18,26 $END $TINKEY parameters /home/seth/gamess/tinker/params/mm3 $END Cheers, Seth Olsen ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Computational Systems Biology Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1(at)uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From chemistry-request@ccl.net Mon Jan 10 11:54:38 2005 Received: from mail.umassmed.edu (edunivsmtp02.umassmed.edu [146.189.194.28]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0AGsbOo004404 for ; Mon, 10 Jan 2005 11:54:37 -0500 Received: from edunivmail01.ad.umassmed.edu ([146.189.193.82]) by mail.umassmed.edu with Microsoft SMTPSVC(6.0.3790.0); Mon, 10 Jan 2005 12:11:12 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: isotope effects-quiver Date: Mon, 10 Jan 2005 12:11:11 -0500 Message-ID: <254B3BAF3C954E42A7074452D80FAF0903957268*at*edunivmail01.ad.umassmed.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: isotope effects-quiver Thread-Index: AcT3N2JMDZ5XsBmyTcSwosEeC9WAfA== From: "Catrina, Irina" To: X-OriginalArrivalTime: 10 Jan 2005 17:11:12.0407 (UTC) FILETIME=[62AE5270:01C4F737] X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 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 j0AGscOo004412 Hi all, I am looking for the QUIVER program (isotope effects calculation from Gaussian output files). Could anybody tell me where I can find it? Thank you very much. Irina From chemistry-request@ccl.net Fri Jan 7 16:28:19 2005 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j07LSIHa004556 for ; Fri, 7 Jan 2005 16:28:18 -0500 Received: by leitl.org (Postfix, from userid 500) id 0E3C93A84DB; Fri, 7 Jan 2005 22:45:28 +0100 (CET) Date: Fri, 7 Jan 2005 22:45:28 +0100 From: Eugen Leitl To: chemistry|at|ccl.net Subject: [Open Babel] New project using OpenBabel (fwd from ernst-georg.schmid|at|bayerbbs.com) Message-ID: <20050107214528.GA17269|at|leitl.org> ----- Forwarded message from ernst-georg.schmid|at|bayerbbs.com ----- From: ernst-georg.schmid|at|bayerbbs.com Date: Wed, 5 Jan 2005 15:09:31 +0100 To: openbabel-discuss|at|lists.sourceforge.net Subject: [Open Babel] New project using OpenBabel Hello, i would like to request an additional entry to the 'Projects using OpenBabel' list on openbabel.sourceforge.net. pgchem::tigress -> http://pgfoundry.org/projects/pgchem/ pgchem::tigress is a chemoinformatics extension to the PostgreSQL DBMS. It enables PostgreSQL to store, retrieve and search chemical datatypes, i.e. Molecules for the time being, by pure SQL statements. It uses checkmol/matchmol and OpenBabel. License is GPL. regards, Ernst-Georg Schmid From chemistry-request@ccl.net Mon Jan 10 14:39:29 2005 Received: from molsoft.com (mail.molsoft.com [64.186.242.98]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0AJdRMa021350 for ; Mon, 10 Jan 2005 14:39:28 -0500 Received: from vega.molsoft.com (vega.molsoft.com [64.186.242.119]) by molsoft.com (8.12.8/8.12.8) with ESMTP id j0AJukav028065 for ; Mon, 10 Jan 2005 11:56:46 -0800 Date: Mon, 10 Jan 2005 11:56:46 -0800 (PST) From: Molsoft LLC To: chemistry:at:ccl.net Subject: MOLSOFT ICM WORKSHOP MARCH 17-18 2005 LA JOLLA CALIFORNIA In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.6 required=7.5 tests=LINES_OF_YELLING,SUBJ_ALL_CAPS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Molsoft LLC would like to announce an ICM workshop entitled "Protein Structure and Drug Discovery" to be held on March 17-18 2005 in La Jolla, CA. The course is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics (www.molsoft.com/training). This course will cover sequence and structure analysis, protein modeling, small molecule docking, protein-protein docking, mutation predictions, simulations, QSAR, ADME-TOX, virtual ligand screening and cheminformatics. The course consists of lectures, demonstrations and "hands-on" computational experiments. "The objective of this training workshop is to help computational chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools." Ruben Abagyan Prof. of Molecular Biology The Scripps Research Institute and Co-Founder of Molsoft LLC Please see our website at www.molsoft.com for more details or e mail info:at:molsoft.com or call (858) 625 2000 ext.108. MolSoft is a San Diego company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. ---------------------------- MolSoft L.L.C. 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 USA Phone: 858 625 2000 (Ext108) Fax: 858 625 2888