From chemistry-request@ccl.net Wed Feb 9 20:30:33 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1A1UWOS024945 for ; Wed, 9 Feb 2005 20:30:32 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j1A1UWcp024943 for chemistry _()_ ccl.net; Wed, 9 Feb 2005 20:30:32 -0500 Date: Wed, 9 Feb 2005 20:30:32 -0500 Message-Id: <200502100130.j1A1UWcp024943 _()_ server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request _()_ ccl.net using -f From: "Vivek, V, Rao" To: chemistry _()_ ccl.net X-Web-Message-Number: 050209202947-24879 Subject: W:g95: free Fortran 95 compiler X-Spam-Status: No, hits=1.0 required=7.5 tests=FORGED_YAHOO_RCVD autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net There is a free Fortran 95 compiler called g95 at http://www.g95.org for Windows, Linux, Mac OS X, and other platforms. It has been used to compile several quantum chemistry and electronic structure programs, including Siesta. Another project to develop a free Fortran 95 compiler is gfortran at http://www.gfortran.org/ . At present there are some features of Fortran 95 that it does not implement. Regards, Vivek Rao Philadelphia From chemistry-request@ccl.net Wed Feb 9 23:07:10 2005 Received: from eos.fwall.u-szeged.hu (eos.fwall.u-szeged.hu [160.114.120.248]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1A478OS001263 for ; Wed, 9 Feb 2005 23:07:09 -0500 Received: from localhost ([127.0.0.1] helo=eos.fwall.u-szeged.hu) by eos.fwall.u-szeged.hu with smtp (Exim 4.34) id 1CyrR4-000418-RK for chemistry _+_ ccl.net; Wed, 09 Feb 2005 13:59:14 +0100 Received: from eos.fwall.u-szeged.hu ([127.0.0.1]) by eos.fwall.u-szeged.hu (SAVSMTP 3.1.0.29) with SMTP id M2005020913591411807 for ; Wed, 09 Feb 2005 13:59:14 +0100 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by eos.fwall.u-szeged.hu with esmtp (Exim 4.34) id 1CyrR4-000413-NT for chemistry _+_ ccl.net; Wed, 09 Feb 2005 13:59:14 +0100 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr _+_ ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id NAA20700 for ; Wed, 9 Feb 2005 13:59:13 +0100 Received: (qmail 10555 invoked by uid 525); 9 Feb 2005 12:59:14 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 9 Feb 2005 12:59:14 -0000 Date: Wed, 9 Feb 2005 13:59:14 +0100 (CET) From: "Dr. Csaba Hetenyi" To: Axel Mathieu cc: chemistry _+_ ccl.net Subject: Re: CCL:EF optimization in MOPAC 7 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-SZTE-local: YES X-SZTE-HU-local: YES X-SZTE-AVcheck: YES X-Spam-Status: No, hits=5.0 required=7.5 tests=COMBINED_FROM,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 I had the same problem. I went one step further and tried to set MAXITR (or stg. like this) to 1000 instead of 200 in the iter.f source and recompiled. This variable is modified by ITRY keyword from the input as i understood. Interestingly, it did not change afterall and stopped at 100 (and not 200 as it should be) iterations. (Compilation was OK.) However, I had no time to make more research in this case. Any solution for the problem is welcome. Best wishes, Csaba On Tue, 8 Feb 2005, Axel Mathieu wrote: > Dear CCL'ers, > > I've been running some AM1 calculations and whenever EF is used it never performs the optimization for more than 100 cycles. I've tried increasing ITRY and CYCLE but it still stays stuck at the default 100 cycles. Am I missing something here? Is this a bug in MOPAC 7? > > Here are the keywords used: XYZ MMOK AM1 T=1D LET GNORM=0.01 NOINTER DUMP=60 EF ITRY=1000 > Thanks for your help ... > > APM > > From chemistry-request@ccl.net Wed Feb 9 23:19:23 2005 Received: from rwcrmhc13.comcast.net (rwcrmhc13.comcast.net [204.127.198.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1A4JKOS001779 for ; Wed, 9 Feb 2005 23:19:20 -0500 Received: from madrid (c-24-18-193-95.client.comcast.net[24.18.193.95]) by comcast.net (rwcrmhc13) with SMTP id <2005021003205201500e7k8ve>; Thu, 10 Feb 2005 03:20:53 +0000 Reply-To: From: "Bob Snyder, ICCS Program Chair" To: "CHMINF-L" , "Computational Chemistry List" , "Medicinal Chemistry List" , "Mol-Diversity" , "ChemWeb List" Cc: "Noordwijkerhout" , "Markus Wagener" Subject: 7th International Conference on Chemical Structures Date: Wed, 9 Feb 2005 19:20:49 -0800 Organization: International Conference on Chemical Structures Message-ID: <001401c50f1f$8551a390$6601a8c0@madrid> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, hits=3.7 required=7.5 tests=FVGT_m_MULTI_ODD2, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Abstract Submission: Abstracts are currently being accepted for the 7th International Conference on Chemical Structures to be held June 5-9, 2005 at the beautiful Congress Center in Noordwijkerhout, The Netherlands. Abstracts may be submitted online at www.int-conf-chem-structures.org/html/abstract_submission.html. Registration: Registration is now open and may be initiated online at www.int-conf-chem-structures.org/html/registration.html. A discount of 175 euro is provided for those registering prior to 15 March 2005. Student Participation: Students may take advantage of a discounted conference fee of 575 euro with early registration and sharing a hotel room. In addition, limited student bursaries are available which can further reduce the conference fee. For additional information see www.int-conf-chem-structures.org/html/student_bursaries.html. Keynote Address: Dr. Johnny Gasteiger will receive the CSA Trust Michael Lynch Award and deliver the keynote address "Chemoinformatics - 30 Years at Noordwijkerhout" Technical Program: The main scientific program will be divided into five plenary sessions: Cheminformatics o representation and searching of conformationally flexible compounds o molecular similarity and diversity o library analysis and profiling o reaction databases and reaction retrieval Structure-Activity and Structure-Property Prediction o modeling of metabolic reactions / reaction networks o prediction of ADME/Tox properties o tautomers in QSAR and Docking Structure-Based Drug Design and Virtual Screening o protein flexibility and homology models in docking o integration of virtual and high-throughput screening o structure- and ligand-based de novo design techniques o improved chemical models and scoring functions Analysis of Large Data Sets o data mining of HTS data sets o analysis of large chemistry spaces o new/emerging methodologies Bridging the Cheminformatics-Bioinformatics Gap o target family based approaches to drug discovery o privileged scaffolds and library design o integrating chemical and biological data spaces Conference presentations will be published in a special issue of the peer-reviewed Journal of Chemical Information and Modeling (JCIM). Posters can be submitted for any of the above and related areas, but we welcome contributions in any aspect of the computer handling of chemical structure information, such as: o representation and manipulation of organic and inorganic compounds, biomacromolecules and polymers o new algorithms for searching and managing chemical structures and reactions o 3D databases and pharmacophore modeling o (automatic) structure elucidation o synthesis planning / synthetic accessibility estimation o combinatorial chemistry, diversity analysis o web technology and its effect on chemical information o electronic publishing o MM or QM/MM simulations Please refer to the conference web site at www.int-conf-chem-structures.org/ for more information. Bob Snyder, ICCS Program Chair Markus Wagener, Vice Chair From chemistry-request@ccl.net Thu Feb 10 02:16:30 2005 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1A7GSOS011707 for ; Thu, 10 Feb 2005 02:16:29 -0500 Received: from caracas-1102.adsl.interware.hu ([213.178.104.78] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.44 #1 (Debian)) id 1Cz8Yu-0005J6-21 for ; Thu, 10 Feb 2005 08:16:28 +0100 Message-ID: <000d01c50f40$b9f19cb0$6401a8c0@cthulhu> From: "Tamas E. Gunda" To: Subject: CCL: Date: Thu, 10 Feb 2005 08:18:21 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1478 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1478 X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net An upgrade is available for the Chemory software. Chemory is a memory game as well as an education tool for everybody interested in chemistry, both for students and professionals. The aim of the puzzle is to turn and match all of the corresponding pairs of cards. Beyond play mode a special reveal (tutorial) mode is available. In this new version the following additions and corrections were made: * Several templates have been refreshed, errors in the namings or drawings have been fixed. Many chemical names were changed according to the latest IUPAC recommendations, however, trivial or old or Beilstein names are also often used. Several new templates have been added to the free version. * A few small improvements and fixes were made in the template creation module (included in the registered version). See at: http://web.interware.hu/frenzy/chemory/ Dr. Tamas E. Gunda tgunda (-AT-) puma.unideb.hu From chemistry-request@ccl.net Thu Feb 10 12:49:55 2005 Received: from prserv.net (out2.prserv.net [32.97.166.32]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1AHns1g018732 for ; Thu, 10 Feb 2005 12:49:54 -0500 Message-Id: <200502101749.j1AHns1g018732 !=! server.ccl.net> Received: from be2.prserv.net (be2.backbone.sch.us[10.254.181.62]) by attglobal.net (out2) with SMTP id <200502101647552020327m36e>; Thu, 10 Feb 2005 16:47:55 +0000 From: jmmckel !=! attglobal.net To: chemistry !=! ccl.net, vivekrao4 !=! yahoo.com Subject: re:CCL:W:g95: free Fortran 95 compiler Date: Thu, 10 Feb 2005 16:47:54 +0000 X-Priority: 3 MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=2.0 required=7.5 tests=NO_REAL_NAME,PRIORITY_NO_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 Hello... Perhaps I missed the earlier discussions on this... Intel has a free Linux fortran compiler that I -think_ is F95 campatible. Regards, John McKelvey From chemistry-request@ccl.net Thu Feb 10 08:55:56 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1ADtt1g003033 for ; Thu, 10 Feb 2005 08:55:55 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j1ADttBf003031 for chemistry^at^ccl.net; Thu, 10 Feb 2005 08:55:55 -0500 Date: Thu, 10 Feb 2005 08:55:55 -0500 Message-Id: <200502101355.j1ADttBf003031^at^server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request^at^ccl.net using -f From: "Richard, , Wood" To: chemistry^at^ccl.net X-Web-Message-Number: 050210085449-2978 Subject: W:CCL:about MM+ ff in Hyperchem X-Spam-Status: No, hits=0.0 required=7.5 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 Hi all, I have a related question. I would like to be able to use HyperChem 5 to build molecules and then save them as *.mol files. Then, I want to read them into Vega ZZ and run mopac on them. My question is this. Is there a format that I can save them as so the charges will be saved and be read into HyperChem? Thanks in advance, Richard