From chemistry-request@ccl.net Thu Aug 28 20:50:51 2003 Received: from smtp4.Stanford.EDU (smtp4.Stanford.EDU [171.67.16.29]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7T0ooUH000867 for ; Thu, 28 Aug 2003 20:50:50 -0400 Received: from alphahelix (alphahelix.Stanford.EDU [171.64.126.26]) by smtp4.Stanford.EDU (8.12.9/8.12.9) with ESMTP id h7T0oieq002412; Thu, 28 Aug 2003 17:50:44 -0700 (PDT) Reply-To: From: "Joseph Han" To: "'Qiang Lu'" Cc: Subject: RE: CCL:install g03 on redhat 7.2 Date: Thu, 28 Aug 2003 17:51:03 -0700 Message-ID: <000601c36dc7$a02e8a70$1a7e40ab@alphahelix> 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 10.0.4024 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4927.1200 In-Reply-To: <1464243755.20030828163127=at=uci.edu> Importance: Normal > > > Hi Joseph, > > I tried to put redhat8 libc.so and libm.so to g03 > directory. Once I run > it. I go the message like: /lib/ld-linux.so.2: version > `GLIBC_PRIVATE` not found (required by .../g03/libc.so.6) > > I think the redhat8 libc.so.6 require /lib/ld-linux.so.2. The > system was compiled under this way. Even I copied redhat > ld-linux.so.2 into g03 directory. It didn't work. > > I wonder how did you bypass this problem. > -- > Best regards, > Qiang mailto:qiangl=at=uci.edu > > I guess that I should clarify. I also copied the following files from the Redhat 8.0 installation into the /share/apps/g03/lib directory: ld-2.2.4.so ld-linux-so.2 ldconfig libcrpyt* Hope this helps. Joseph From chemistry-request@ccl.net Fri Aug 29 04:41:33 2003 Received: from albert.unito.it (albert.unito.it [130.192.119.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7T8fVUH001283 for ; Fri, 29 Aug 2003 04:41:32 -0400 Received: (from root@localhost) by albert.unito.it (8.12.9/8.12.9-PostNaja) id h7T8fTFN028939 for chemistry=at=ccl.net; Fri, 29 Aug 2003 10:41:29 +0200 Received: from unito.it (chpc666.ch.unito.it [130.192.137.66]) by albert.unito.it (8.12.9/8.12.9-PostNaja) with ESMTP id h7T8fSDG028893 for ; Fri, 29 Aug 2003 10:41:28 +0200 Message-ID: <3F4F12D9.8030405=at=unito.it> Date: Fri, 29 Aug 2003 10:46:17 +0200 From: Piero Ugliengo User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; 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: IR intensity conversion factor Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-scanner: scanned by Inflex 1.0.12.3 Dear netters, I would like to know the exact formula that Gaussian98 is using to convert the square of derivative of the dipole moment with respect to a displacement into the IR intensity in KM/mol. Thank you all Piero Ugliengo _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex From chemistry-request@ccl.net Fri Aug 29 05:17:54 2003 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7T9HrUH004217 for ; Fri, 29 Aug 2003 05:17:54 -0400 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.2 #30546) id <01L015VU01U8002VO8=at=cuces.unisi.it> for chemistry=at=ccl.net; Fri, 29 Aug 2003 11:17:47 +0100 (MET) Received: from unisi.it (ccmaol10.chim.unisi.it [172.16.53.96]) by cuces.unisi.it (PMDF V6.2 #30546) with ESMTPA id <01L015VRQ3DA002SIY=at=cuces.unisi.it>; Fri, 29 Aug 2003 11:17:47 +0100 (MET) Date: Fri, 29 Aug 2003 11:08:27 +0200 From: "Nicolas Ferre'" Subject: Gaussian03: BOMD Sender: ferre=at=unisi.it To: chemistry=at=ccl.net, help=at=gaussian.com Message-id: <3F4F180B.2A7F3833=at=unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.78iC-CCK-MCD [en_US] (X11; U; AIX 5.1) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi, I'd like to know a little bit more about running Born-Oppenheimer MD in g03. First, is it possible to carry on MDs without informations about the Hessian ? Unfortunately, the GradientOnly keyword does not seem to work, but I found the corresponding IOp: 1/71=-1. Anyway, even if I include this IOp, the job starts with the calculation of an analytical Hessian. By the way, is it possible to switch to a numerical one ? At first sight, it seems that a first job devoted to the calculation of the numerical Hessian must be done, then that this Hessian should be read at the beginning of the MD using IOp(1/10=5). Is it the only way ? Last question: is it possible to freeze the position of some atoms ? Alternatively, is it possible to add some point charges ? That's all for now. Thanks for any light. Nicolas -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre=at=unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@ccl.net Fri Aug 29 09:07:36 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7TD7RUH022647 for ; Fri, 29 Aug 2003 09:07:30 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Fri, 29 Aug 2003 10:09:38 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56BB6=at=correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: CCL: Problems with degrees of Freedom Date: Fri, 29 Aug 2003 10:09:38 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h7TD7aUH022658 Dear CCLers, On carrying out a hindered internal rotation analysis on an ethylbenzene radical I get the reply from G98w that there is a problem with the number of degrees of freedom. How can I over come this problem? Any suggestions would be extremely welcome. I have included an edited out put and I will produce a summary for he group. Thanks Ian Cut lines.................. %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. %chk=ethylbenzene radical1.chk Default route: MaxDisk=2000MB -------------------------------------------------------------------- # freq=(noraman,readfc,readiso,hindered) uhf/6-31+g(d) geom=allcheck Cut lines..................... Rotating electric field derivatives to standard orientation. Rotating nuclear coordinate derivatives to standard orientation. Atom 1 has atomic number 6 and mass 12.00000 Cut lines.................. Atom 17 has atomic number 1 and mass 1.00783 Full mass-weighted force constant matrix: Low frequencies --- -0.2932 -0.1931 -0.0010 -0.0003 0.0001 0.3171 Low frequencies --- 37.1659 145.2276 165.9155 Hindered Internal Rotation Analysis Internal coordinate list checked Check for planar centers 1 2 6 7 360.000 2 1 3 8 360.000 3 2 4 12 359.993 4 3 5 9 360.000 5 4 6 10 360.000 6 1 5 11 360.000 15 12 16 17 358.261 Check reduced barrier height. Cut-off : V/RT = 33.7559 Check for ring deformation Number of internal rotation degrees of freedom = 2 NNew= 36 NTest= 2 NB= 8 IFrz= 0 IBar= 0 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in d:\G98W\l716.exe. Job cpu time: 0 days 0 hours 0 minutes 3.0 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 8 Scr= 1 Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cijncia e da Tecnologia- MCT Avenida Ipj, No 900 - Cidade Universitaria Ilha do Fundco Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell=at=cetem.gov.br From chemistry-request@ccl.net Fri Aug 29 12:35:13 2003 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7TGZDUH000714 for ; Fri, 29 Aug 2003 12:35:13 -0400 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 06D969928; Fri, 29 Aug 2003 18:35:12 +0200 (CEST) To: amber..at..scripps.edu, pdb-l..at..rcbs.org, chemistry..at..ccl.net Subject: AmberFFC v1.3 released Message-ID: <1062174912.3f4f80c0e62d8..at..webmail.u-picardie.fr> Date: Fri, 29 Aug 2003 18:35:12 +0200 (CEST) From: FyD Cc: fduprado..at..scripps.edu MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, I am pleased to announce the release of AmberFFC version 1.3. In its original version, AmberFFC was designed to convert six AMBER force fields (parm91, parm91X, parm94, parm96, parm98 & parm99) freely available in the public domain (http://amber.scripps.edu & http://amber.scripps.edu/dbase.html), for use with commercial molecular modeling packages, using the Accelrys (http://www.accelrys.com/) software package as a case model. With the version 1.2, AmberFFC converts three GLYCAM force fields (GLYCAM_93 and two new GLYCAM versions) developed by Woods et al. (http://glycam.ccrc.uga.edu). With the version 1.3, a modification of the parm99 version (Simmerling et al.) and the GAFF force fields are also converted. The AmberFFC web site has slightly changed: http://www.u-picardie.fr/labo/lbpd/AmberFFC/ Regards, Francois From chemistry-request@ccl.net Fri Aug 29 13:49:15 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h7THnEUH002498 for ; Fri, 29 Aug 2003 13:49:15 -0400 Received: from DAVEG-LIFEBOOK.cachesoftware.com (netscreen.cachesoftware.com [12.17.172.74]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h7THhpI26257; Fri, 29 Aug 2003 10:43:51 -0700 Message-Id: <5.2.1.1.0.20030829094315.02504580..at..mail.cachesoftware.com> X-Sender: daveg..at..mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Fri, 29 Aug 2003 10:38:58 -0700 To: chemistry..at..ccl.net From: David Gallagher Subject: CCL: 3D-Auto-stereoscopic Laptop for computational chemistry Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed 3D "Auto-stereoscopic" Laptop for computational chemistry Sharp have just announced a novel 3D "auto-stereoscopic" laptop computer. This 2.8GHz Pentium based machine display true 3D-stereoscopic images without the need for any special glasses. The 3D-stereo can be instantly switched on or off and is built in to the patented 15" XGA display. A special application from DDD Inc. allows you to turn your own photos and PowerPoint slides into 3D-stereo. The laptop will also run specially processed Movies and Games in 3D-stereo. This new Windows-XP laptop running the complete suite of CAChe computer-aided chemistry software in full 3D-stereo will be demonstrated for the first time at the ACS in New York at the CAChe booths (945 & 947) 8th - 10th September. For more information and introductory offer contact sales..at..cachesoftware.com. David Gallagher CAChe Group, Fujitsu.