From chemistry-request@ccl.net Wed Jun 11 00:17:50 2003 Received: from atc.atccu.chula.ac.th (atc.atccu.chula.ac.th [192.207.64.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5B4Hnkr025590 for ; Wed, 11 Jun 2003 00:17:49 -0400 Received: (from nobody@localhost) by atc.atccu.chula.ac.th (8.9.3/8.9.3) id LAA09403; Wed, 11 Jun 2003 11:41:05 +0700 Date: Wed, 11 Jun 2003 11:41:05 +0700 Message-Id: <200306110441.LAA09403*at*atc.atccu.chula.ac.th> From: "Nadtanet Nunthaboot" To: chemistry*at*ccl.net Subject: X-ray of dioxobutanoic acid X-Mailer: NeoMail 1.25 X-IPAddress: 192.207.64.59 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 -- NeoMail - Webmail that doesn't suck... as much. http://neomail.sourceforge.net I want X-ray structures or coordinate of dioxobutanoic acid or 4-(3- Benzylphenyl)-2,4-dioxobutanoic acid (diketo group).Annnybody,can you help me? Nadtanet Nunthaboot (nadtanet*at*atc.atccu.chula.ac.th) From chemistry-request@ccl.net Wed Jun 11 04:00:25 2003 Received: from out.esrf.fr (firewall.ill.fr [193.49.43.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5B80Okr032240 for ; Wed, 11 Jun 2003 04:00:25 -0400 Received: (from uucp@localhost) by out.esrf.fr (1.0.0) id h5B80MN27752 for ; Wed, 11 Jun 2003 10:00:23 +0200 (MEST) Received: from esrf.esrf.fr(160.103.2.9) by firewall via smap (V1.3) id tmp027701; Wed Jun 11 10:00:08 2003 Subject: Spin-Orbit Received: from leeloo.esrf.fr (localhost [127.0.0.1]) by esrf.esrf.fr (8.9.0/8.9.0) with ESMTP id KAA09889 for ; Wed, 11 Jun 2003 10:00:07 +0200 (MET DST) Message-Id: <5.1.0.14.0.20030611095251.00af71a8-.at.-mailserv.esrf.fr> X-Sender: vetere-.at.-mailserv.esrf.fr X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 11 Jun 2003 10:00:12 +0200 To: chemistry-.at.-ccl.net From: Valentina VETERE Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear all, I'm looking for a Spin-orbit code that works with open-shell electrons, on molecular wavefunctions, in a non-relativistic limit and that give rice to monoconfigurational (1-determinant) wavefunction .. Any idea???? valentina From chemistry-request@ccl.net Wed Jun 11 03:29:59 2003 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5B7Twkr031196 for ; Wed, 11 Jun 2003 03:29:59 -0400 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id KAA14068; Wed, 11 Jun 2003 10:23:00 +0200 (CEST) Date: Wed, 11 Jun 2003 10:23:00 +0200 (CEST) Message-Id: <200306110823.KAA14068-.at.-oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib-.at.-oc30.uni-paderborn.de using -f From: Ingo Brunberg To: weiz-.at.-mail.rochester.edu CC: johns-.at.-ks.uiuc.edu, chemistry-.at.-ccl.net In-reply-to: <3ee685de.5133.27812-.at.-mail.rochester.edu> (weiz-.at.-mail.rochester.edu) Subject: Re: CCL:vmd under windows References: <3ee685de.5133.27812-.at.-mail.rochester.edu> Looks like VMD has problems with spaces in the path. I guess your VMD installation is rooted somewhere under C:\Program Files\. Try to install it in a location that has no whitespace in its path. Regards, Ingo Brunberg > Dear Sir: > > I want to use vmd to make some pictures for my paper, but I only have > linux and windows system.when I used vmd under linux and render the > picture into ps format, it lost most of the fanzy effect, the picture > looks ugly. when I switch to windows machine and render the picture to > "snapshot", it looks very good. however, some other problems come, I > actually have a trajectory saved in xyz format, in linux, vmd can read all > of them and show the movie, but under windows it can not even read one > snapshot, the error message is > *********************** > Invalid switch - "tmp". > 'C:\Program' is not recognized as an internal or external command,operable > program or batch file. > ERROR> Could not read file ...... > ************************ > > can you give me some hint about this? > > Wei From chemistry-request@ccl.net Wed Jun 11 05:05:28 2003 Received: from mserv.itpa.lt (mserv.itpa.lt [193.219.53.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5B95Rkr002974 for ; Wed, 11 Jun 2003 05:05:28 -0400 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.9/8.12.6) with ESMTP id h5B95Hk3045663; Wed, 11 Jun 2003 12:05:22 +0300 (EEST) (envelope-from tamulis.-at-.mserv.itpa.lt) Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.12.9/8.12.6/Submit) with ESMTP id h5B95BCB045660; Wed, 11 Jun 2003 12:05:12 +0300 (EEST) Date: Wed, 11 Jun 2003 12:05:10 +0300 (EEST) From: Arvydas Tamulis To: Valentina VETERE cc: chemistry.-at-.ccl.net Subject: Re: CCL:Spin-Orbit In-Reply-To: <5.1.0.14.0.20030611095251.00af71a8.-at-.mailserv.esrf.fr> Message-ID: <20030611120422.U45298-100000.-at-.mserv.itpa.lt> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Ask my former student Zilvinas Rinkevicius: rinkevic.-at-.TheoChem.kth.se On Wed, 11 Jun 2003, Valentina VETERE wrote: > Dear all, > > > I'm looking for a Spin-orbit code that works with open-shell electrons, on > molecular wavefunctions, in a non-relativistic limit and that give rice to > monoconfigurational (1-determinant) wavefunction .. > > Any idea???? > > valentina > > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY.-at-.ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl.-at-.ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed Jun 11 08:20:05 2003 Received: from wrzx98.rz.uni-wuerzburg.de (wrzx98.rz.uni-wuerzburg.de [132.187.3.98]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5BCK4kr008964 for ; Wed, 11 Jun 2003 08:20:05 -0400 Received: from wrzx30.rz.uni-wuerzburg.de (wrzx30.rz.uni-wuerzburg.de [132.187.1.30]) by wrzx98.rz.uni-wuerzburg.de (Postfix) with ESMTP id F053D9DD for ; Wed, 11 Jun 2003 14:20:03 +0200 (CEST) Received: from virusscan (localhost [127.0.0.1]) by wrzx30.rz.uni-wuerzburg.de (Postfix) with ESMTP id 2E52D4599A for ; Wed, 11 Jun 2003 14:19:59 +0200 (CEST) Received: from wrzx07.rz.uni-wuerzburg.de ([132.187.1.7]) by virusscan (wrzx30 [132.187.1.30:25]) (amavisd-new) with ESMTP id 21099-03 for ; Wed, 11 Jun 2003 14:19:59 +0200 (CEST) Received: from spamchecker (localhost [127.0.0.1]) by spamcheck.rz.uni-wuerzburg.de (Postfix) with ESMTP id 267E99161 for ; Wed, 11 Jun 2003 14:19:58 +0200 (CEST) Received: from wocx51.chemie.uni-wuerzburg.de (wocx51.chemie.uni-wuerzburg.de [132.187.64.51]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id 11321571D for ; Wed, 11 Jun 2003 14:19:58 +0200 (CEST) Received: from chemie.uni-wuerzburg.de (wocd73.chemie.uni-wuerzburg.de [132.187.64.173]) by wocx51.chemie.uni-wuerzburg.de (SGI-8.9.3/8.9.3/uniwue-M-1.0) with ESMTP id OAA51914 for ; Wed, 11 Jun 2003 14:19:57 +0200 (MESZ) Message-ID: <3EE72071.CB69285B..at..chemie.uni-wuerzburg.de> Date: Wed, 11 Jun 2003 14:28:33 +0200 From: Bernd Engels X-Mailer: Mozilla 4.78 [de] (Windows NT 5.0; U) X-Accept-Language: de MIME-Version: 1.0 To: ccl Subject: solvent effects Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=-13.8 required=8.0 tests=BAYES_01,LOCAL_CLIENT,LOCAL_SENDER,NICE_HELO, USER_AGENT_MOZILLA_XM autolearn=ham version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) X-Virus-Scanned: by amavisd-new (Rechenzentrum Universitaet Wuerzburg) Hi, I am looking for an implementation of the COSMO approach (or another one) for MP2. Bernd -- Prof. Dr. Bernd Engels Institut f|r Organische Chemie Bayerische Julius-Maximilians-Universitdt W|rzburg Am Hubland D- 97074 W|rzburg Tel.: ++49 (0)931 - 888 - 5394 Fax: ++49 (0)931 - 888 - 4606 e-mail: bernd..at..chemie.uni-wuerzburg.de From chemistry-request@ccl.net Wed Jun 11 04:47:02 2003 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5B8l2kr002461 for ; Wed, 11 Jun 2003 04:47:02 -0400 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Wed, 11 Jun 2003 09:46:59 +0100 Date: Wed, 11 Jun 2003 09:46:59 +0100 Message-ID: <3EA4FB980003A820..at..hawk.dcu.ie> In-Reply-To: <3ee685de.5133.27812..at..mail.rochester.edu> From: noel.oboyle2..at..mail.dcu.ie Subject: RE: vmd under windows To: "weiz" Cc: chemistry..at..ccl.net MIME-Version: 1.0 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 h5B8l2kr002462 Hello I understand the problem with the Windows version. It's because certain, ah, old, programs still have problems understanding folder names containing spaces. You have probably installed VMD into "C:\Program Files\...." but it cannot understand the space in "Program Files" and is looking for "C:\Program". You should uninstall it, and reinstall it into a folder called "C:\Programs" or something like that. Hopefully that will help BTW, you can make even nicer pictures by rendering as a POV file. You need to download POVRAY from the web. I have made some very nice pictures. :-) Noel >-- Original Message -- >From: "weiz" >To: johns..at..ks.uiuc.edu >Cc: chemistry..at..ccl.net >Subject: CCL:vmd under windows >Date: Tue, 10 Jun 2003 21:29:02 -0400 > > >Dear Sir: > >I want to use vmd to make some pictures for my paper, but I only have >linux and windows system.when I used vmd under linux and render the >picture into ps format, it lost most of the fanzy effect, the picture >looks ugly. when I switch to windows machine and render the picture to >"snapshot", it looks very good. however, some other problems come, I >actually have a trajectory saved in xyz format, in linux, vmd can read all >of them and show the movie, but under windows it can not even read one >snapshot, the error message is >*********************** >Invalid switch - "tmp". >'C:\Program' is not recognized as an internal or external command,operable >program or batch file. >ERROR> Could not read file ...... >************************ > >can you give me some hint about this? > >Wei From chemistry-request@ccl.net Wed Jun 11 04:29:22 2003 Received: from aspirine.u-strasbg.fr (aspirine.u-strasbg.fr [130.79.84.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5B8TLkr002046 for ; Wed, 11 Jun 2003 04:29:22 -0400 Received: from aspirine.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id h5B8ONq32762 for ; Wed, 11 Jun 2003 10:24:23 +0200 Sender: mkrier..at..aspirine.u-strasbg.fr Message-ID: <3EE6DFEB.1FF7F210..at..aspirine.u-strasbg.fr> Date: Wed, 11 Jun 2003 09:53:16 +0200 From: Mireille Krier Organization: ULP-CNRS UMR 7081 X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry..at..ccl.net Subject: CCL: ISIS/BASE import limit Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello CCLers, I was wondering if there is a import limit of structures from an SDFile to a local ISIS/BASE (not ISIS HOST)? In other words, is there a fixed number that one can not exceed? ( I have ISIS/BASE 2.3)? Thanks in advance. Mireille -- +--------------------------------------------------------------+ Mireille KRIER Bioinformatique du medicament, Equipe 5 du Laboratoire de Pharmacochimie et de la communication cellulaire UMR 7081 ULP-CNRS Faculti de Pharmacie 74, route du Rhin -B.P. 60024 F-67401 Illkirch CEDEX, France +--------------------------------------------------------------+ From chemistry-request@ccl.net Wed Jun 11 11:26:22 2003 Received: from qtp.ufl.edu (entry.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5BFQLkr015212 for ; Wed, 11 Jun 2003 11:26:21 -0400 Received: from pc1 (ntred1 [128.227.192.113]) by qtp.ufl.edu (8.12.8/8.12.8/Server/deumens) with SMTP id h5BFQGNF011451; Wed, 11 Jun 2003 11:26:17 -0400 (EDT) Message-ID: <058d01c3302f$4408cf10$71c0e380!at!qtp.ufl.edu> From: "Stefan Fau" To: "Tanja van Mourik" Cc: "CCL - all" References: <200305311224.h4VCOvG18404!at!socrates-a.ucl.ac.uk> Subject: Re: CCL:charge densities Date: Wed, 11 Jun 2003 11:36:41 -0400 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Tanja, ACES II calculates the electron density for CCSD(T). You may contact Dr. Perera (perera!at!qtp.ufl.edu) for technical questions. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau!at!qtp.ufl.edu University of Florida | (352) 392-6714 Quantum Theory Project 2319 NPB #92, P.O.Box 118435 Gainesville, FL 32611-8435 From chemistry-request@ccl.net Wed Jun 11 10:48:26 2003 Received: from ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5BEmQkr014422 for ; Wed, 11 Jun 2003 10:48:26 -0400 Received: from moline.ks.uiuc.edu (moline.ks.uiuc.edu [130.126.120.60]) by ks.uiuc.edu (8.12.9/8.11.2) with ESMTP id h5BEmQVn005003; Wed, 11 Jun 2003 09:48:26 -0500 (CDT) Received: (from johns@localhost) by moline.ks.uiuc.edu (8.11.6+Sun/8.9.1) id h5BEmPB25308; Wed, 11 Jun 2003 09:48:25 -0500 (CDT) Date: Wed, 11 Jun 2003 09:48:25 -0500 From: John Stone To: Ingo Brunberg Cc: weiz)at(mail.rochester.edu, chemistry)at(ccl.net Subject: Re: CCL:vmd under windows Message-ID: <20030611094823.C25210)at(moline.ks.uiuc.edu> References: <3ee685de.5133.27812)at(mail.rochester.edu> <200306110823.KAA14068)at(oc30.uni-paderborn.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <200306110823.KAA14068)at(oc30.uni-paderborn.de> User-Agent: Mutt/1.3.19i Hi, Do you have Babel installed on your windows machine? The previous versions of VMD (i.e. prior to the almost-release 1.8.1 version I'm working on now) did not have a built-in XYZ reader, so they require the use of Babel. If you don't have babel installed, then you still be unable to load your XYZ file, regardless of the issue with spaces in the filenames. If you'd like to try the new version, let me know, it loads XYZ files directly without the need for babel. Thanks, John Stone vmd)at(ks.uiuc.edu On Wed, Jun 11, 2003 at 10:23:00AM +0200, Ingo Brunberg wrote: > Looks like VMD has problems with spaces in the path. I guess your VMD > installation is rooted somewhere under C:\Program Files\. Try to > install it in a location that has no whitespace in its path. > > Regards, > Ingo Brunberg > > > Dear Sir: > > > > I want to use vmd to make some pictures for my paper, but I only have > > linux and windows system.when I used vmd under linux and render the > > picture into ps format, it lost most of the fanzy effect, the picture > > looks ugly. when I switch to windows machine and render the picture to > > "snapshot", it looks very good. however, some other problems come, I > > actually have a trajectory saved in xyz format, in linux, vmd can read all > > of them and show the movie, but under windows it can not even read one > > snapshot, the error message is > > *********************** > > Invalid switch - "tmp". > > 'C:\Program' is not recognized as an internal or external command,operable > > program or batch file. > > ERROR> Could not read file ...... > > ************************ > > > > can you give me some hint about this? > > > > Wei -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns)at(ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@ccl.net Wed Jun 11 10:04:15 2003 Received: from web21108.mail.yahoo.com (web21108.mail.yahoo.com [216.136.227.110]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5BE4Ekr012525 for ; Wed, 11 Jun 2003 10:04:14 -0400 Message-ID: <20030611140414.93845.qmail)at(web21108.mail.yahoo.com> Received: from [203.197.89.222] by web21108.mail.yahoo.com via HTTP; Wed, 11 Jun 2003 07:04:14 PDT Date: Wed, 11 Jun 2003 07:04:14 -0700 (PDT) From: Gurpreet Singh Subject: CCL:Optimization To: chemistry)at(ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, We are trying to do an optimization of the x-ray Hydrogen positions of alanine (for example) and compare them to Neutron Diffraction data using Gaussian98. However, the output (Input Orientation or Standard Orientation) is not in the same format (ie fractional or cartesian coordinates) as that of the x-ray/neutron diffraction data. In the calculation, some of the larger atoms (ie Carbon and Nitrogen ) are frozen (ie not to be optimized) and we do not want those coordinates to change. They are supposed to remain invariant. Is there any way to get the Gaussian output in fractional/cartesian coordinates so as to compare with the input file? Thank YOu Gurpreet Singh Project Assistant, National Chemical Laboratory, Pune, India From chemistry-request@ccl.net Wed Jun 11 08:45:59 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 h5BCjwkr009698 for ; Wed, 11 Jun 2003 08:45:59 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Wed, 11 Jun 2003 09:48:46 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B5E)at(correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: CCL: Freq calculation, software limitation? Date: Wed, 11 Jun 2003 09:48:44 -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 h5BCjxkr009699 Dear CCLers, I am carrying out a frequency calculation on a large molecule, 150 atoms using G98w, and HF/3-21g* method and level respectively. It is writing out the AO integrals to the *.rwf files which I have set up. Altogether I have set up 7 rwf files each of 36MW in size. The calculation runs out of stipulated *.rwf file space. Which means that my calculation is trying to generate more than 12.9 GB of data. I have stipulated an 8th. rwf file which it has not used so I am assuming that the limit of rwf files one can use in the route statement is 7. Have I really reached the limit of G98w capabilities or is there a way round this? TIA 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 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell)at(cetem.gov.br From chemistry-request@ccl.net Tue Jun 10 09:10:23 2003 Received: from mefteh.dsi.univ-paris5.fr (mefteh.dsi.univ-paris5.fr [193.51.86.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5ADAMkr004961 for ; Tue, 10 Jun 2003 09:10:23 -0400 Received: (from root@localhost) by mefteh.dsi.univ-paris5.fr (8.11.6) id h5ADAKM23887; Tue, 10 Jun 2003 15:10:20 +0200 (MEST) Received: from alpha.univ-paris5.fr (alpha.univ-paris5.fr [193.51.86.2]) by mefteh.dsi.univ-paris5.fr (8.11.6) with ESMTP id h5ADAFu23827; Tue, 10 Jun 2003 15:10:15 +0200 (MEST) Received: from pcumr70.biomedicale.univ-paris5.fr (pcumr70.biomedicale.univ-paris5.fr [172.20.101.107]) by alpha.univ-paris5.fr (8.9.3p2/jtpda-5.3.1) with ESMTP id PAA02538 ; Tue, 10 Jun 2003 15:10:14 +0200 (MET DST) Subject: Re: helix axis for A-RNA From: =?ISO-8859-1?Q?Teletch=E9a_St=E9phane?= To: Vlad Cojocaru Cc: CCL , amber , VMD In-Reply-To: <3EE5CE25.9070700-.at.-mpi-bpc.mpg.de> References: <3EE5CE25.9070700-.at.-mpi-bpc.mpg.de> Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="=-C8b79/aIt09yj0DxSbUE" X-Mailer: Ximian Evolution 1.0.8-3.1mdk Date: 10 Jun 2003 15:11:35 +0200 Message-Id: <1055250695.18746.8.camel-.at.-pcumr70.biomedicale.univ-paris5.fr> Mime-Version: 1.0 X-Virus-Scanned: by AMaViS perl-11 --=-C8b79/aIt09yj0DxSbUE Content-Type: text/plain; charset=ISO-8859-15 Content-Transfer-Encoding: quoted-printable Le mar 10/06/2003 =E0 14:25, Vlad Cojocaru a =E9crit : > Dear coleagues, > I have an RNA molecule that comprises two helical regions and one=20 > loop and I would like to follow the agle between the 2 helices during an=20 > MD trajectory. I was thinking to represent the helical axis of the two=20 > helices and then calculate the angle between the 2 axis. I was trying=20 > with VMD to represent the helical axis but yet I didnt have a lot of=20 > success. If somebody knows how coould one define and represent the=20 > helical axis of an A type RNA helix within VMD or other software I would=20 > kindly appreciate any suggestions. > Best wishes, > vlad >=20 Curves will allow you to calculate such an axis, and is now widely recognised as a reference algorithm for such a purpose (for example NDB tool for providing helical parameters uses Curves). You can find it at : http://www.ibpc.fr/UPR9080/Curindex.html You can after visualize it in vmd. To calculate the angle between two is implicit, since Curves involves the calculation of the overall angle of the molecule, you can simply substract them. Stef --=20 *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~* Teletch=E9a St=E9phane - CNRS UMR 8601 Lab. de chimie et biochimie pharmacologiques et toxicologiques 45 rue des Saints-P=E8res 75270 Paris cedex 06 t=E9l : (33) - 1 42 86 20 86 - fax : (33) - 1 42 86 83 87 m=E9l : steletch-.at.-biomedicale.univ-paris5.fr *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~* Linux 2.4.19-32mdk #1 Tue Mar 25 20:45:38 MST 2003 3:00pm up 43 days, 3:37, 5 users, load average: 1.09, 1.36, 1.40 --=-C8b79/aIt09yj0DxSbUE-- From chemistry-request@ccl.net Wed Jun 11 15:40:11 2003 Received: from ccl.net (email.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5BJeBkr022346 for ; Wed, 11 Jun 2003 15:40:11 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h5BJeBg25287; Wed, 11 Jun 2003 15:40:11 -0400 (EDT) Date: Wed, 11 Jun 2003 15:40:09 -0400 (EDT) From: Jan Labanowski To: chemistry=at=ccl.net cc: Jan Labanowski , Amiram Goldblum Subject: 03.06.11 One Week Job in Jerusalem in July -- Teach Sybyl Software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Message-Id: <5.1.0.14.0.20030611170912.03d31d90=at=vms.huji.ac.il> Date: Wed, 11 Jun 2003 17:14:33 +0200 To: Jan Labanowski From: Amiram Goldblum Subject: 03.06.11 One Week Job in Jerusalem in July -- Teach Sybyl Software We are looking for a Tripos software expert who may be willing to come for a week to Israel to teach a group of scientists (about 20) the basics of Sybyl and its various functions. Teaching will be on SGIs, preferably in July. Candidates (references may be requested) should contact Prof. Amiram Goldblum ASAP. Cordially, Amiram Goldblum ************************************************************************* Amiram Goldblum, Ph.D. Cell: 972-54-653292 Professor of Medicinal Chemistry Tel: 972-2-6758701 Molecular Modeling and Drug Design Fax: 972-2-6758925 Department of Medicinal Chemistry and Natural Products School of Pharmacy, Hebrew University of Jerusalem ISRAEL 91120 email: amiram=at=vms.huji.ac.il Internet: http://www.md.huji.ac.il/models/ ************************************************************************* From chemistry-request@ccl.net Wed Jun 11 12:37:26 2003 Received: from cougar.it.wsu.edu (cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5BGbPkr017330 for ; Wed, 11 Jun 2003 12:37:25 -0400 Received: from tyr0.chem.wsu.edu (tyr0.chem.wsu.edu [134.121.44.19]) by cougar.it.wsu.edu (8.12.9/8.12.9) with ESMTP id h5BGbKZ1214092; Wed, 11 Jun 2003 09:37:20 -0700 (PDT) Date: Wed, 11 Jun 2003 09:37:19 -0700 Subject: Re: CCL:Spin-Orbit Content-Type: text/plain; delsp=yes; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v552) Cc: chemistry(at)ccl.net To: Valentina VETERE From: Kirk Peterson In-Reply-To: <5.1.0.14.0.20030611095251.00af71a8(at)mailserv.esrf.fr> Message-Id: Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.552) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) X-Spam-Status: No, hits=-3.9 required=6.0 tests=CARRIAGE_RETURNS,DEAR_SOMEBODY,FROM_WSU,IN_REP_TO, QUOTED_EMAIL_TEXT,SPAM_PHRASE_03_05,USER_AGENT_APPLEMAIL version=2.43 X-Spam-Level: Dear Valentina, either Gamess or Molpro will do what you would like. best wishes, Kirk Peterson On Wednesday, June 11, 2003, at 01:00 AM, Valentina VETERE wrote: > Dear all, > > > I'm looking for a Spin-orbit code that works with open-shell > electrons, on molecular wavefunctions, in a non-relativistic limit and > that give rice to monoconfigurational (1-determinant) wavefunction .. > > Any idea???? > > valentina > > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY(at)ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl(at)ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > > -------------------------------------------- Kirk A. Peterson Associate Professor Department of Chemistry Washington State University Pullman, WA 99164-4630 Office: (509) 335-7867 Fax: (509) 335-8867 kipeters(at)wsu.edu http://tyr0.chem.wsu.edu/~kipeters/ ------------------------------------------------------------------------ From chemistry-request@ccl.net Wed Jun 11 14:15:11 2003 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 h5BIFAkr019917 for ; Wed, 11 Jun 2003 14:15:11 -0400 Received: by lgdx04.lg.ehu.es id UAA0000027688; Wed, 11 Jun 2003 20:15:04 +0200 (MET DST) Message-ID: <001601c33045$60ce10e0$222fe39e-.at.-lc.ehu.es> From: "Pablo Vitoria" To: "CCL" , Subject: Different results in Gamess (Linux) and PC Gamess. Date: Wed, 11 Jun 2003 20:15:02 +0200 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0012_01C33056.2413BD60" 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 This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C33056.2413BD60 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0013_01C33056.2413BD60" ------=_NextPart_001_0013_01C33056.2413BD60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I recently installed the last version of Gamess on my dual AMD Athlon = box (Linux, Mandrake 9.0, gcc 3.2, with the BLAS library recomended). I = run all the tests (all of them terminated normally), and the results = agreed with the ones in the header of the .inp files, so I guess the = compilation went OK. But in order to do some benchmarking (and gain experience with the = program) I downloaded some input files that I found in the web. I attach = one example (taxol.inp). The job ends normally but the result is not = exactly the one in the file: INPUT CARD>! FINAL 6-31G* energy=3D -2911.8558097425 after 14 = iterations =20 FINAL RHF ENERGY IS -2911.8558059245 AFTER 14 ITERATIONS Besides, exactly the same job on PC Gamess (running either under Linux = or W98) gives: INPUT CARD>! FINAL 6-31G* energy=3D -2911.8558097425 after 14 = iterations =20 FINAL ENERGY IS -2911.8558097427 AFTER 14 ITERATIONS The same happens with several other jobs.=20 Does anyone have an idea about why this happens?=20 Thank you very much for your help Pablo Vitoria -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qu=EDmica Inorg=E1nica, Facultad de Ciencias Universidad del Pa=EDs Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6015992 Fax. 94 4648500 ------=_NextPart_001_0013_01C33056.2413BD60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
 
I recently installed the last version = of Gamess on=20 my dual AMD Athlon box (Linux, Mandrake 9.0, gcc 3.2, with the BLAS = library=20 recomended). I run all the tests (all of them terminated normally), and = the=20 results agreed with the ones in the header of the .inp files, so I guess = the=20 compilation went OK.
 
But in order to do some benchmarking = (and gain=20 experience with the program) I downloaded some input files that I found = in the=20 web. I attach one example (taxol.inp). The job ends normally but the = result is=20 not exactly the one in the file:
 
 INPUT CARD>!   FINAL = 6-31G*=20 energy=3D -2911.8558097425 after 14=20 iterations          &nb= sp;       =20
 FINAL RHF ENERGY IS    -2911.8558059245 = AFTER  14=20 ITERATIONS
Besides, exactly the same job on PC = Gamess (running=20 either under Linux or W98) gives:
 
 INPUT CARD>!   FINAL = 6-31G*=20 energy=3D -2911.8558097425 after 14=20 iterations          &nb= sp;       =20
 FINAL ENERGY IS    -2911.8558097427 AFTER  = 14=20 ITERATIONS
 
The same happens with several other = jobs.=20
 
Does anyone have an idea about why this = happens?=20
 
Thank you very much for your help
 
Pablo Vitoria
 
--------------------------------------------------------
Pabl= o Vitoria=20 Garcia
Dpto. Qu=EDmica Inorg=E1nica, Facultad de = Ciencias
Universidad del Pa=EDs=20 Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)
 
Tfno. 94 6015992
Fax. 94=20 4648500
------=_NextPart_001_0013_01C33056.2413BD60-- ------=_NextPart_000_0012_01C33056.2413BD60 Content-Type: text/plain; name="taxol.inp" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="taxol.inp" =0A= ! AM1 gradient of Taxol (C O NH ) (save the yew trees!)=0A= ! 47 14 51=0A= !=0A= ! For isolation of natural product and structure, see=0A= ! M.C.Wani, et al. J.Am.Chem.Soc. 1971, 93, 2325-2327.=0A= ! For total synthesis, see K.C.Nicolaou, et al. =0A= ! J.Am.Chem.Soc. 1995, 117, 615-23, 624-33, 634-44, 645-52.=0A= ! For a popular summary, =0A= ! S.Borman Chem.Eng.News 1991, Sept 2, pg 11.=0A= !=0A= ! FINAL E=3D -419.3072472399, 14 iters, RMS=3D0.000002614=0A= ! This run takes 237 seconds on a RS/6000 m350 (13 Mar 95)=0A= !=0A= ! FINAL 6-31G* energy=3D -2911.8558097425 after 14 iterations=0A= ! 6-31G* RMS gradient=3D 0.020898909, 113 atoms, 1032 AOs =0A= ! This run takes 1260 minutes on 4 Sun E450 300 MHz nodes (1 May 98)=0A= !=0A= ! Caution: this AM1 structure has not been double checked to =0A= ! be sure it has the right stereochemistry.=0A= !=0A= $contrl scftyp=3Drhf runtyp=3Dgradient coord=3Dzmt $end=0A= =0A= ! input for semiempirical run:=0A= --- $system memory=3D1200000 timlim=3D1000 $end=0A= --- $basis gbasis=3Dam1 $end=0A= =0A= ! input for ab initio run:=0A= $system memory=3D11000000 timlim=3D5000 $end=0A= $basis gbasis=3Dn31 ngauss=3D6 ndfunc=3D1 $end=0A= $scf dirscf=3D.true. $end=0A= =0A= $guess guess=3Dhuckel $end=0A= $data=0A= taxol...RHF/AM1 structure (E=3D-419.307247, pos. def., ZPE=3D591.8)=0A= c1=0A= C =0A= C 1 1.5057200=0A= C 2 1.5614445 1 104.2234295=0A= C 3 1.5714997 2 111.7151479 1 67.7312058 0=0A= C 4 1.5494125 3 117.9172407 2 -79.2800040 0=0A= C 5 1.5595168 4 114.3061717 3 109.8716232 0=0A= C 6 1.5424391 5 106.8050834 4 -96.6488358 0=0A= C 1 1.4963282 2 124.8223822 3 -115.0658293 0=0A= C 5 1.5363437 4 110.8729873 3 -117.7991527 0=0A= C 9 1.5635746 5 118.3767553 4 -165.5518602 0=0A= C 10 1.4976308 9 115.3953466 5 4.4726871 0=0A= C 6 1.5718251 5 115.6270498 4 147.0893678 0=0A= C 1 1.3602731 2 117.2386796 3 58.8728310 0=0A= O 3 1.4280992 2 105.1273808 1 -177.2779708 0=0A= C 3 1.5339183 2 110.7834907 1 -60.0220786 0=0A= C 13 1.5024683 1 118.1243855 2 -10.1092353 0=0A= C 13 1.4791267 1 124.2040287 2 171.6786244 0=0A= C 6 1.5223018 5 114.6103166 4 25.1463169 0=0A= O 12 1.4125265 6 112.7055108 5 -101.7694166 0=0A= O 10 1.4637758 9 90.4698173 5 120.0752402 0=0A= C 9 1.5570073 5 119.4839481 4 -63.9315350 0=0A= O 7 1.2372634 6 120.0605178 5 -107.7333075 0=0A= C 2 1.5205200 1 117.3809847 8 7.9740076 0=0A= O 8 1.4245267 1 115.1246894 2 -14.4065641 0=0A= H 5 1.1345117 4 106.1448019 3 -6.2503391 0=0A= O 9 1.4262797 5 103.8506751 4 67.7759774 0=0A= O 4 1.4459630 3 102.9731997 2 159.5208692 0=0A= C 2 1.5432342 1 109.4482939 8 127.5305866 0=0A= O 16 1.4498850 13 107.1454617 1 -155.4204941 0=0A= H 14 0.9667433 3 107.3865731 2 175.2316377 0=0A= H 19 0.9641087 12 109.4844429 6 78.8933701 0=0A= C 24 1.3773637 8 118.6322264 1 -107.3665583 0=0A= C 26 1.3687156 9 123.0323717 5 -176.6347503 0=0A= C 27 1.3758092 4 118.3479524 3 -120.3747418 0=0A= C 29 1.3627988 16 117.8761516 13 -153.5297631 0=0A= H 28 1.1165177 2 110.7787398 1 115.7319748 0=0A= H 28 1.1160336 2 111.1684644 1 -6.0921133 0=0A= H 28 1.1176318 2 110.8807513 1 -125.5300683 0=0A= H 23 1.1194022 2 108.6291380 1 -176.8191436 0=0A= H 23 1.1181638 2 109.7652894 1 64.0138760 0=0A= H 23 1.1111578 2 113.7410967 1 -56.5537116 0=0A= H 18 1.1200514 6 109.7284859 5 164.7276655 0=0A= H 18 1.1188049 6 110.0266850 5 46.1188931 0=0A= H 18 1.1124733 6 112.6070640 5 -76.3842140 0=0A= H 17 1.1186891 13 111.2139389 1 -164.1929435 0=0A= H 17 1.1208819 13 110.4333681 1 75.5977675 0=0A= H 17 1.1199002 13 110.7819648 1 -44.0844311 0=0A= H 11 1.1221645 10 109.3618557 9 -79.6715595 0=0A= H 11 1.1230610 10 109.0956017 9 161.7859051 0=0A= H 21 1.1107276 9 115.4242518 5 127.6565870 0=0A= H 21 1.1131139 9 114.8091206 5 -5.5196945 0=0A= H 12 1.1358630 6 107.2936174 5 147.3388600 0=0A= H 16 1.1283555 13 110.3509914 1 87.2272035 0=0A= H 8 1.1383288 1 108.4871474 2 -136.7531621 0=0A= H 15 1.1247713 3 108.7848853 2 -102.8211982 0=0A= H 15 1.1216486 3 109.4747085 2 140.5976786 0=0A= H 10 1.1156715 9 114.2885627 5 -128.8649651 0=0A= H 4 1.1245191 3 106.4765134 2 45.9217969 0=0A= O 33 1.2283273 26 120.9576752 9 -3.1138348 0=0A= C 33 1.4934473 26 111.0121181 9 177.0990449 0=0A= H 60 1.1180137 33 108.7651688 26 -81.3797632 0=0A= H 60 1.1167592 33 109.1795950 26 159.1306485 0=0A= H 60 1.1170784 33 110.5013092 26 38.0363399 0=0A= O 34 1.2336713 27 118.5519795 4 -13.8226485 0=0A= C 34 1.4705397 27 113.8279934 4 167.3812851 0=0A= C 65 1.4020287 34 118.3054966 27 172.5881000 0=0A= C 66 1.3936542 65 119.7308150 34 179.4573894 0=0A= C 67 1.3952163 66 120.1312902 65 -0.1134240 0=0A= C 68 1.3958010 67 120.1356082 66 0.0025781 0=0A= C 65 1.4000741 34 121.5957664 27 -8.1117243 0=0A= H 66 1.1024483 65 119.4501211 34 -0.4081223 0=0A= H 67 1.1003756 66 119.7721814 65 179.9002487 0=0A= H 68 1.1007319 67 119.9532681 66 -179.9911986 0=0A= H 69 1.1000428 68 119.9979823 67 -179.9101537 0=0A= H 70 1.1015613 65 119.6991139 34 0.7922344 0=0A= C 1 8.4991998 2 102.7919793 3 49.7803710 0=0A= C 76 1.5056911 1 30.9911390 2 52.8494395 0=0A= C 35 1.5209024 29 111.3692178 16 175.4183200 0=0A= C 76 1.4024677 77 117.5591395 78 153.9651017 0=0A= C 79 1.3928014 76 120.3051201 77 -175.9295789 0=0A= C 80 1.3954367 79 120.0902003 76 0.1618077 0=0A= C 81 1.3936610 80 119.7873662 79 -0.5472043 0=0A= C 76 1.3969350 77 122.9709854 78 -22.3818369 0=0A= O 78 1.4102089 35 110.3344336 29 -45.4398905 0=0A= N 77 1.4338346 76 116.9566145 79 -72.2260549 0=0A= O 35 1.2306238 29 119.9579703 16 -5.6455142 0=0A= C 85 1.3873338 77 130.8121540 76 -46.4333123 0=0A= O 87 1.2488265 85 116.3912970 77 -165.9992599 0=0A= C 87 1.4875354 85 123.0496696 77 17.4608437 0=0A= C 89 1.3991021 87 119.1249016 85 98.7582517 0=0A= C 90 1.3941818 89 119.7335987 87 174.3384362 0=0A= C 91 1.3950928 90 120.1388063 89 -0.5427199 0=0A= C 92 1.3946208 91 120.0225575 90 0.2674803 0=0A= C 89 1.3976132 87 120.3660516 85 -87.4065225 0=0A= H 77 1.1450419 76 105.2527707 79 43.1732452 0=0A= H 78 1.1281267 35 107.4743254 29 74.9018422 0=0A= H 79 1.1008124 76 119.7532287 77 4.2365455 0=0A= H 80 1.0999388 79 119.8579729 76 -179.8440413 0=0A= H 81 1.0998466 80 120.0702604 79 179.7247288 0=0A= H 82 1.1000004 81 120.0666930 80 -179.3376100 0=0A= H 83 1.1019960 76 120.2206007 77 -6.0817187 0=0A= H 84 0.9687775 78 107.4503230 35 55.6777737 0=0A= H 85 1.0037983 77 112.6254224 76 153.8021574 0=0A= H 90 1.1001563 89 119.9973791 87 -5.0758401 0=0A= H 91 1.0997211 90 119.7858581 89 179.8853150 0=0A= H 92 1.0998733 91 119.9701455 90 -179.4901717 0=0A= H 93 1.0996950 92 120.0743077 91 -179.6569002 0=0A= H 94 1.1015718 89 119.9438327 87 6.2987557 0=0A= C 32 1.4891558 24 111.6912760 8 -178.9182038 0=0A= O 32 1.2291675 24 119.2037372 8 0.9339276 0=0A= H 109 1.1181405 32 108.8706166 24 87.8419315 0=0A= H 109 1.1174644 32 110.4292040 24 -31.8392077 0=0A= H 109 1.1170483 32 109.1321596 24 -152.8295913 0=0A= $end=0A= =0A= ------=_NextPart_000_0012_01C33056.2413BD60--