From chemistry-request@server.ccl.net Sat Dec 11 11:12:24 1999 Received: from janus.rz.uni-konstanz.de (janus.rz.uni-konstanz.de [134.34.3.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA23713 for ; Sat, 11 Dec 1999 11:12:23 -0500 Received: from stevieray (actually stevieray.biologie.uni-konstanz.de) by janus.rz.uni-konstanz.de with Intranet with SMTP; Sat, 11 Dec 1999 16:00:09 +0100 Message-Id: <3.0.3.32.19991211155808.009747a0@popserver.uni-konstanz.de> X-Sender: pop04225@popserver.uni-konstanz.de X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Sat, 11 Dec 1999 15:58:08 +0100 To: chemistry@server.ccl.net From: Frank Neese Subject: Amide vibrational frequencies Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi all, I would appreciate if somebody could point me to a recent discussion of the vibrational properties of amides. I'm especially interested in what is known about the ability of B3LYP to reproduce the harmonic frequencies and normal modes of this functional group. Thanks in advance, I'll summarize the answers Frank ----------------------------------------- ! Dr. Frank Neese ! ! Fakultaet fuer Biologie ! ! Universitaet Konstanz ! ! D-78457 Konstanz ! ! Germany ! ! e-mail: Frank.Neese@uni-konstanz.de ! ! Tel : 07531/883205 ! ! FAX : 07531/882966 ! ----------------------------------------- From chemistry-request@server.ccl.net Fri Dec 10 18:04:28 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA19176 for ; Fri, 10 Dec 1999 18:04:28 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id QAA08274; Fri, 10 Dec 1999 16:57:12 -0500 (EST) Date: Fri, 10 Dec 1999 16:57:12 -0500 (EST) From: Iraj Daizadeh To: Jan Labanowski cc: Ricardo Grau Crespo , chemistry@ccl.net Subject: Re: CCL:column editor In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Emacs...fine... For a nicer interface try the freeware product: nedit latent on sgi....to pick out columns use the control-mouse (index1 for righthanders)... iraj. > For simple things the good old emacs has colum functions: > M-x kill-rectangle > M-x yank-rectangle > You mark the rectangular region (from mark to current cursor), kill it, > (i.e., cut it out), move the cursor where you want it placed > and yank it. Of course, you can kill it, and not yank it, if you only > want to delete text. > > Jan > > Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 > Ohio Supercomputer Center | Internet: jkl@ccl.net > 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html > Columbus, OH 43212-1163 | http://www.ccl.net/ > > n Fri, 10 Dec 1999, Iraj Daizadeh wrote: > > > > > Interesting query... > > > > For multiple alignments editors require in a most direct way your > > interests...please check the following--for example... > > > > http://www.ibcp.fr/mpsa > > > > First transform your data into the following form: > > > > > > > 150109492812 > > > > > 10328283823 > > > > > 39183923023043 > > > > or > > > > > > > agtctgtctttct > > > > > agcttttcttctc > > > > I am only guessing that it can perform the same column functions with > > numbers as well...--doubt it in retrospect....this is not excel.... > > > > please summarize--ricardo..... > > > > iraj. > > > > Iraj Daizadeh, Ph.D. > > Harvard University > > Department of Cellular and Molecular Biology > > The Biological Laboratories > > 16 Divinity Avenue > > Cambridge, MA 02138 > > Phone: (617) 495-0783 > > (617) 495-0560 > > Fax: (617) 496-4313 > > Email: daizadeh@nucleus.harvard.edu > > WebPage: http://mcb.harvard.edu/gilbert/daizadeh > > > > > > On Fri, 10 Dec 1999, Ricardo Grau Crespo wrote: > > > > > Hi CCL, > > > Could you please tell if there is any editor for Linux that allows > > > working (inserting, deleting, moving, etc) with data columns. And, if > > > yes, where can I find it? > > > Excuse me if this is not strictly a computational chemistry question, > > > but I need to know that for working with input and output files of my > > > calculations. > > > Thank you very much in advance, > > > Ricardo. > > > > > > -- > > > ************************************************************** > > > * Ricardo Grau Crespo * > > > * Catalysis Department, Center for Petroleum Research. * > > > * Washington # 169. Cerro, Havana, CUBA * > > > ************************************************************** > > > > > > > From chemistry-request@server.ccl.net Sat Dec 11 07:38:01 1999 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA23037 for ; Sat, 11 Dec 1999 07:38:01 -0500 Received: from neriserv.chim.unisi.it (piccittre.bio-mol.unisi.it [192.167.127.4]) by unisi.it (PMDF V5.2-32 #31247) with ESMTP id <01JJDIWJCLCY001H48@unisi.it> for chemistry@www.ccl.net; Sat, 11 Dec 1999 12:28:17 MET Date: Sat, 11 Dec 1999 13:29:25 +0100 From: Andrea Bernini Subject: Re: CCL:column editor Sender: andrea@unisi.it To: Ricardo Grau Crespo , Computational Chemistry list Message-id: <385243A5.283F97B4@neriserv.chim.unisi.it> Organization: Diparttimento Biologia Molecolare MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.5-15 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en, it References: <385125AF.8C5BFDE@ceinpet.inf.cu> Ricardo Grau Crespo wrote: > > Hi CCL, > Could you please tell if there is any editor for Linux that allows > working (inserting, deleting, moving, etc) with data columns. And, if > yes, where can I find it? > Excuse me if this is not strictly a computational chemistry question, > but I need to know that for working with input and output files of my > calculations. > Thank you very much in advance, > Ricardo. > In standard Linux distribution you can find joe. It is a console editor such as vi but more user-friendly, and it has rectangular block selection features, search man pages for "rectangular" and "define block". Andrea. ____________________________________________ Dr. Andrea Bernini, Ph.D. Molecular Biology Dept. University of Siena Via Fiorentina 1, 53100 Siena, Italy Phone +39 577 234911 Fax +39 577 234903 From chemistry-request@server.ccl.net Sat Dec 11 10:55:30 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA23649 for ; Sat, 11 Dec 1999 10:55:30 -0500 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id PAA27305; Sat, 11 Dec 1999 15:44:56 +0100 From: Jochen Küpper Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Ricardo Grau Crespo , "chemistry@ccl.net" Subject: Re: CCL:column editor Date: Sat, 11 Dec 1999 15:42:08 +0100 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <385125AF.8C5BFDE@ceinpet.inf.cu> In-Reply-To: <385125AF.8C5BFDE@ceinpet.inf.cu> MIME-Version: 1.0 Message-Id: <99121115445601.27293@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id KAA23650 On Fre, 10 Dez 1999 Ricardo Grau Crespo wrote: > Could you please tell if there is any editor for Linux that allows >working (inserting, deleting, moving, etc) with data columns. And, if >yes, where can I find it? XEmacs, of course (or plain emacs as well) :-) It's called rectangles in their nomenclature. Try hitting and select some stuff using your mouse - to give you an easy beginning. -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Sat Dec 11 13:19:49 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA24687 for ; Sat, 11 Dec 1999 13:19:49 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id MAA08558; Sat, 11 Dec 1999 12:12:43 -0500 (EST) Date: Sat, 11 Dec 1999 12:12:43 -0500 (EST) From: Iraj Daizadeh To: "Przemyslaw G. Czyryca" cc: chemistry@ccl.net Subject: Re: CCL:column editor In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This is indeed a fantastic finding....Thanks iraj... > On Fri, 10 Dec 1999, Ricardo Grau Crespo wrote: > > > Could you please tell if there is any editor for Linux that allows > > working (inserting, deleting, moving, etc) with data columns. And, if > > yes, where can I find it? > > In your linux distribution :-). Linux's vi is in fact a link to vim - an > improved version of vi. In vim selecting of a column may be done with > cursor arrows after ctrl-v combination. Then deleting with 'd' and so on > (as always - man vi). > > Przemek G. Czyryca > Utah State University > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Sat Dec 11 13:59:00 1999 Received: from web113.yahoomail.com (web113.yahoomail.com [205.180.60.84]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA24924 for ; Sat, 11 Dec 1999 13:59:00 -0500 Received: (qmail 28623 invoked by uid 60001); 11 Dec 1999 17:48:53 -0000 Message-ID: <19991211174853.28622.qmail@web113.yahoomail.com> Received: from [206.148.0.101] by web113.yahoomail.com; Sat, 11 Dec 1999 09:48:53 PST Date: Sat, 11 Dec 1999 09:48:53 -0800 (PST) From: "Eric S. Ball" Subject: Re: CCL:RO jobs on unsaturated organometallics To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii A hearty thank you to all for the large number and greatly helpful emails regarding my situation. I'm looking into the various tips offered. When I have worked through this I will post a summary of the suggestions and highlight the solution I find with the help that has been graciously offered by so many. Best wishes for the impending new year, Eric Ball ------------------------------------- ! University of Wisconsin - Madison ! ! esbchem@yahoo.com ! ------------------------------------- My original follows for those that may still find it of interest: --- "Eric S. Ball" wrote: > Greetings, > > I'm having great difficulty getting convergence for my > restricted open-shell DFT jobs on coordinatively unsaturated > iron compounds. I'm using Jaguar for these (rob3lyp/lacvp**), > and I've used G94/98 in the past, so suggestions pertaining to > either package would help. In Jaguar I've used vshifts of 0.2 > - > 1.0; accuracy settings (iacc) of quick, medium, and ultrafine; > As per hints in the manual I tried iacc=1 (ultrafine grids) > with > the lac3vp** basis (largest available) and etot simply > oscillated. > > If anyone has successfully dealt with a similar situation with > either Jaguar or G98, I'd love to start a little dialog. > If/when I meet with success I'll edit down any conversations > to > the pertinent points and repost them. > > Thanks in advance, > Eric Ball __________________________________________________ Do You Yahoo!? Thousands of Stores. Millions of Products. All in one place. Yahoo! Shopping: http://shopping.yahoo.com From chemistry-request@server.ccl.net Sat Dec 11 15:48:54 1999 Received: from Mailer.Uni-Marburg.DE (Mailer.Uni-Marburg.DE [137.248.1.76]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA25336 for ; Sat, 11 Dec 1999 15:48:53 -0500 Received: from pc16163.pharmazie.uni-marburg.de (mppp008.ppp.Uni-Marburg.DE [193.174.76.136]) by Mailer.Uni-Marburg.DE (AIX4.3/8.9.3/8.9.3) with ESMTP id UAA43346 for ; Sat, 11 Dec 1999 20:39:05 +0100 Received: from pc16154.pharmazie.uni-marburg.de (pc16165.pharmazie.uni-marburg.de [137.248.161.165]) by pc16163.pharmazie.uni-marburg.de (8.9.3/8.9.3) with ESMTP id UAA29542 for ; Sat, 11 Dec 1999 20:30:17 +0100 Message-ID: <3852A643.3CDD48AB@pc16154.pharmazie.uni-marburg.de> Date: Sat, 11 Dec 1999 20:30:11 +0100 From: Dirk Dettmering Organization: AK Imming und EDV-Abteilung - FB Pharmazie, Uni Marburg X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: de,en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: column editor 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 PAA25337 Hy Ricardo, try kwrite from the KDE project (should come with your favourite distribution in one of the kde-rpms, otherwise try www.kde.org). This is my own favourite lightwhight editor: small, fast and you don't have to remember tons of key combinations! You can mark columns with your mouse! Yust my 2 cent! Dirk Dettmering BTW: I coukdn't send you this directly ----- The following addresses had transient non-fatal errors ----- --- The transcript of the session follows --- ... Deferred: The connection is refused by ceniai.net.cu. Ricardo Grau Crespo wrote: > > Hi CCL, > Could you please tell if there is any editor for Linux that allows > working (inserting, deleting, moving, etc) with data columns. And, if > yes, where can I find it? > Excuse me if this is not strictly a computational chemistry question, > but I need to know that for working with input and output files of my > calculations. > Thank you very much in advance, > Ricardo. -- ==================D=i=r=k===D=e=t=t=m=e=r=i=n=g=================== Email: Dettmer@pc16154.pharmazie.uni-marburg.de http://pc16154.pharmazie.uni-marburg.de/dettmering/index.html Tel.: +49 6421 28 25824 Fax: +49 6421 28 25828 Philipps-Universität Marburg - FB Pharmazie und Lebensmittelchemie Philipps University Marburg - Germany - Department of Pharmacy This message was written entirely with recycled electrons ================================================================== Fight Spam! Join EuroCAUCE: http://www.euro.cauce.org --