From chemistry-request@ccl.net Wed Jan 14 17:33:58 2004 Received: from postal.usc.edu (postal.usc.edu [128.125.253.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0EMXuc1009046 for ; Wed, 14 Jan 2004 17:33:56 -0500 Received: from usc.edu (localhost.usc.edu [127.0.0.1]) by postal.usc.edu (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HRI00ALL41PSE=at=postal.usc.edu> for chemistry=at=ccl.net; Wed, 14 Jan 2004 14:34:37 -0800 (PST) Received: from [128.125.23.1] by postal.usc.edu (mshttpd); Wed, 14 Jan 2004 14:34:37 -0800 Date: Wed, 14 Jan 2004 14:34:37 -0800 From: jeffrey raber Subject: Autodock - Autogrid3 Authentication To: chemistry=at=ccl.net Message-id: MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) Content-type: text/plain; charset=us-ascii Content-language: en Content-transfer-encoding: 7BIT Content-disposition: inline X-Accept-Language: en Priority: normal X-Spam-Status: No, hits=0.0 required=7.0 tests=HOT_NASTY 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 everyone. I am sorry if this question has been answered before, but the archive search is currently down. Can anyone inform me as to how I can fix an Authentication issue using autogrid3 (part of autodock, which I am using through autodock tools). The authenticity of host 'xxx.xxx.xxx' (xxx.xxx.xx.x)' can't be established. RSA key fingerprint is 3f:eb:79:0a:61:31:82:69:46:53:ed:06:51:f8:3b:74. Are you sure you want to continue connecting (yes/no)? yes Host key verification failed. I did have a successful calculation, but it asked me for my password 3 times before it was complete. Is this normal? It is certainly annoying, and I want to see if I can avoid it. I tried changing the host script to use localhost (127.0.0.1), but that didn't work either, I got the same authentication error. Any help in this matter is greatly appreciated. -Jeffrey Raber jraber=at=usc.edu From chemistry-request@ccl.net Wed Jan 14 19:19:38 2004 Received: from mtiwmhc12.worldnet.att.net (mtiwmhc12.worldnet.att.net [204.127.131.116]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0F0Jbc1013934 for ; Wed, 14 Jan 2004 19:19:37 -0500 Received: from zinc.fujitsu.com (201.denver-05rh15-16rt.co.dial-access.att.net[12.73.180.201]) by worldnet.att.net (mtiwmhc12) with SMTP id <2004011500201711200pmlvje>; Thu, 15 Jan 2004 00:20:18 +0000 Message-Id: <6.0.1.1.2.20040114171434.02c98398-.at.-postoffice.worldnet.att.net> X-Sender: mrmopac-.at.-postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Version 6.0.1.1 Date: Wed, 14 Jan 2004 17:18:39 -0700 To: chemistry-.at.-ccl.net From: "James J. P. Stewart" Subject: re. CCL:increasing optimization cycles in Mopac Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=2.6 required=7.0 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS 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 >Rajarshi Guha asks: >Hi, > I'm trying to do a geometry optimization with Mopac 7.04. The keywords >I have specified are > >pm3 t=999999.9 ef hess=1 mmok let gnorm= > >However the cacluation does not end properly and I get the error: > >EXCESS NUMBER OF OPTIMIZATION CYCLES > >Looking through the Mopac manual I dont see anyway to increase the >number of optimization cycles. Does anybody know how can I increase the >number of cycles so that I can achieve the SCF field? Optimization cycles in MOPAC refer to geometry optimization, not to generating a self-consistent field. The job is apparently running correctly. I forget if MOPAC 7 supported the keyword "CYCLES=n", but you might try adding "CYCLES=99999" Jimmy Stewart From chemistry-request@ccl.net Wed Jan 14 20:24:48 2004 Received: from smtp3.Stanford.EDU (smtp3.Stanford.EDU [171.67.16.117]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0F1Olc1014926 for ; Wed, 14 Jan 2004 20:24:47 -0500 Received: from cardinal5.Stanford.EDU (cardinal5.Stanford.EDU [171.64.15.253]) by smtp3.Stanford.EDU (8.12.10/8.12.10) with ESMTP id i0F1PSGX013904; Wed, 14 Jan 2004 17:25:28 -0800 Received: from cardinal5.Stanford.EDU (localhost.localdomain [127.0.0.1]) by cardinal5.Stanford.EDU (8.12.10/8.12.10) with ESMTP id i0F1PROp025676; Wed, 14 Jan 2004 17:25:27 -0800 Received: (from gorelsky@localhost) by cardinal5.Stanford.EDU (8.12.10/8.12.8/Submit) id i0F1PQE8025675; Wed, 14 Jan 2004 17:25:26 -0800 Date: Wed, 14 Jan 2004 17:25:26 -0800 (PST) From: "S.I.Gorelsky" To: Vladimir Khavryutchenko cc: CHEMISTRY)at(ccl.net Subject: Re: CCL:d-orbitals and transition metals in semiempirical methods In-Reply-To: <000a01c3daea$68d77920$0400000a)at(compchem.kiev.ua> Message-ID: MIME-Version: 1.0 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 I believe the most recent review about semiempirical methods for transition metals can be found in Comprehensive Coordination Chemistry-II, T. J. Meyer, J. A. McCleverty, Eds.; Elsevier: 2003, Vol. 2, Chapter 2.38, pp 467-489. This book has been published only a few weeks ago. Regarding the SINDO and MSINDO methods, here is the link: http://www.theochem.uni-hannover.de/software.html You can ask the authors for a copy of the software. With regards, S. Gorelsky On Thu, 15 Jan 2004, Vladimir Khavryutchenko wrote: > Dear CCL'ers > > I am interested in d-orbitals and transition metals in the modern semiempirical quantum chemical methods and their realizations. If anyone knows of the good articles, reviews and so on, please, inform me and, if it is possible, send me a copy or file. We have some difficulty with scientific journals and books last 15 years. > If anyone knows of the method, introduced into MOPAC6/7 for the transition metals? There is not parameterization for these elements, but the parameter set is available from HyperChemT 7 from Hypercube, Inc. The parameter's files are not marked as copyrighted. Evaluation copy of HyperChemT 7 can compute some transition metal compounds, but there are not any references about used method, due to Stewart's PM3 method was designed for sp-basis only. Up to me, it means that all results, obtained using HyperChemT 7 for transition metal compounds can not be discussed due to unpublished and undescribed method was applied. > > If anyone knows of the sites or other open sources for the SINDO and MSINDO method, please, inform me too. It is a pity, that new method developing is only for the commercial software. LINUX history is a good example for the collective developing of the complicated software. > I'll be happy to know more about this and, if these problems are interesting, I'll post the replies. I am ready to discuss these problems directly. > > > > Thank you in advance, > Vladimir > > > VladimirKhavryutchenko > PhD in chemistry > Computation Chemistry Group > Institute for Sorbtion and Problem of Endoecology > National Academy of Science of Ukraine, Kiyv > UKRAINE > Phone: +38(044)563-42-74 > e-mail: vkhavr)at(compchem.kiev.ua > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0553. ---------------------------------------------------------------- From chemistry-request@ccl.net Thu Jan 15 07:20:39 2004 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0FCKbc1027551 for >ccl.net>; Thu, 15 Jan 2004 07:20:38 -0500 Received: by lgdx04.lg.ehu.es id NAA0000001036; Thu, 15 Jan 2004 13:21:19 +0100 (MET) Message-ID: <002901c3db62$13255ec0$222fe39e<>lc.ehu.es> From: "Pablo Vitoria" >lg.ehu.es> To: "CCL" >ccl.net> Subject: Gaussian 03 Compilation with IFC (again) Date: Thu, 15 Jan 2004 13:21:16 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 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 Hi, A couple of months ago I asked in this list about the possibility of compiling G03 with Intel Fortran Compiler (ifc), and I sent a summary of the (few) answers saying that it is possible, although not supported by Gaussian Inc. Well, this e-mail is to inform that in the updates download section of Intel (http://premier.intel.com), in the "File description" it says "This compiler build has been certified for usage with Gaussian 03" for versions 7.1.037 and 8.0.038 (and above I guess), released at the end of 2003. I think that is good news! On the other hand, in the Gaussian page nothing has changed: the only supported Fortran compiler seems to be Portland Gropu F77. Best regards Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qummica Inorganica, Facultad de Ciencias Universidad del Pams Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6015992 Fax. 94 4648500 From chemistry-request@ccl.net Thu Jan 15 15:51:35 2004 Received: from ultra.chem.ucsb.edu (ultra.chem.ucsb.edu [128.111.114.119]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0FKpYc1008407 for ; Thu, 15 Jan 2004 15:51:34 -0500 Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id DC0745028A; Thu, 15 Jan 2004 12:52:14 -0800 (PST) Received: from ultra.chem.ucsb.edu ([127.0.0.1]) by localhost (ultra [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 19864-07; Thu, 15 Jan 2004 12:52:14 -0800 (PST) Received: by ultra.chem.ucsb.edu (Postfix, from userid 3016) id 0847A50289; Thu, 15 Jan 2004 12:52:14 -0800 (PST) Received: from localhost (localhost [127.0.0.1]) by ultra.chem.ucsb.edu (Postfix) with ESMTP id 01ED017070C; Thu, 15 Jan 2004 12:52:13 -0800 (PST) Date: Thu, 15 Jan 2004 12:52:13 -0800 (PST) From: John Bushnell To: Pablo Vitoria Cc: CCL Subject: Re: CCL:Gaussian 03 Compilation with IFC (again) In-Reply-To: <002901c3db62$13255ec0$222fe39e/at/lc.ehu.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new 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 This may just refer to the Itanium/Linux platform, which does in fact show the Intel Fortran and ecc compilers in the source code table at gaussian.com. - John On Thu, 15 Jan 2004, Pablo Vitoria wrote: > Hi, > > A couple of months ago I asked in this list about the possibility of > compiling G03 with Intel Fortran Compiler (ifc), and I sent a summary of the > (few) answers saying that it is possible, although not supported by Gaussian > Inc. > Well, this e-mail is to inform that in the updates download section of Intel > (http://premier.intel.com), in the "File description" it says "This compiler > build has been certified for usage with Gaussian 03" for versions 7.1.037 > and 8.0.038 (and above I guess), released at the end of 2003. I think that > is good news! > On the other hand, in the Gaussian page nothing has changed: the only > supported Fortran compiler seems to be Portland Gropu F77. > > Best regards > > Pablo > > -------------------------------------------------------- > Pablo Vitoria Garcia > Dpto. Qummica Inorganica, Facultad de Ciencias > Universidad del Pams Vasco (UPV/EHU) > Aptdo. 644 > 48080 Bilbao (Bizkaia) > > Tfno. 94 6015992 > Fax. 94 4648500 From jkl@ccl.net Thu Jan 15 18:05:46 2004 -0500 Message-ID: <01c601c3dbb9$6f90d020$2c03a8c0..at..qct.fq.oc.uh.cu> From: reynier..at..fq.uh.cu To: chemistry..at..ccl.net Subject: CCL: Software to build topology files for Gromos automatically? Date: Thu, 15 Jan 2004 16:46:34 -0600 Hi I'm trying to use Gromos to performed a MD of some small molecules. Does anybody knows about a software to automaticaly build the topology files for moleculos non known by Gromos? Regards Reynier