From chemistry-request@server.ccl.net Tue Nov 23 00:17:07 1999 Received: from mailhost.det.ameritech.net (mpdr0.detroit.mi.ameritech.net [206.141.239.206]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA20426 for ; Tue, 23 Nov 1999 00:17:07 -0500 Received: from quantumnt ([206.141.209.226]) by mailhost.det.ameritech.net (InterMail v4.01.01.07 201-229-111-110) with SMTP id <19991123041025.GGGL800.mailhost.det.ameritech.net@quantumnt>; Mon, 22 Nov 1999 23:10:25 -0500 Message-ID: <001f01bf3568$aaec5870$0300a8c0@quantumnt> From: "Jim Kress" To: "Deepak Singh" , "Computational Chemistry List" References: <383A0193.6E70DA22@syr.edu> Subject: Re: CCL:AVS/IBM explorer followup Date: Mon, 22 Nov 1999 23:10:24 -0500 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 You might want to try: http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm It's not free but it will do most if not all of what you want. Jim Check out my web site http://www.kressworks.com/ ----- Original Message ----- From: Deepak Singh To: Computational Chemistry List Sent: Monday, November 22, 1999 9:53 PM Subject: CCL:AVS/IBM explorer followup > Thank you to everyone who replied to the following post > > ----------------------- > > Hi, > > I have been looking into software (for IRIX) that will allow me to > visualize MO's, charge densities etc. I heard a lot about AVS but that > seems to have disappeared. I ran into IBM's 'Open Visualization Data > Explorer' today and it seems to be similar to AVS. I would like to know > > if people have used this a lot with G98/94, GAMESS and MOPAC? Is the > performance similar to AVS? > > ------------------------ > > I think I should clarify a few things. When I say AVS has disappeared, > I mean the "Application Visualization System"produced by produced by > Advanced Visual Systems which used to have a "chemistry" viewer. I > found this at the following site > > http://www.arl.hpc.mil/PET/cta/ccm/training/courses/scivis/AVS/AVS-schedule. html > > > > I might be wrong but as someone did point out to me, AVS express does > not have the chemistryu module per se. Some people wrote to me about > MOLDEN, which is what I use now, but molden cannot give me the quality > of graphics which I require. It is great as a reference and research > tool, but we have always used something like "mathematica" to get better > graphics . > > The IBM explorer seems to be a similar product to AV, and it is FREE. > I tried getting it running today but had a bunch of compilation > trouble. I would not like to spend too much time on it, if people have > had trouble with it. In short, I guess what I need to know is that, on > a SGI, which product would give me the best quality graphics for G98, > MOPAC and GAMESS output, without unnecessary headaches. I have no > personal bias. Just a note gopenmol is good, but seems better for MD > analysis. > > Deepak. > > > > -- > ********************************************************************** > Deepak Singh Tel : (315)443 1739 (w) > Graduate Student (315)472 9659 (h) > Dept. of Chemistry Fax : (315)443 4070 > Syracuse University email : desingh@syr.edu > 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh > NY 13244 > > "Violence is the last refuge of the incompetent." --- Salvor Hardin > ********************************************************************** > > > > > -= 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 Mon Nov 22 16:47:02 1999 Received: from ozone.umsl.edu (ozone.umsl.edu [134.124.105.185]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA18095 for ; Mon, 22 Nov 1999 16:47:02 -0500 Received: from ozone.umsl.edu (indy1.umsl.edu [134.124.105.162]) by ozone.umsl.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id QAA07029 for ; Mon, 28 Jun 1999 16:28:07 -0700 Sender: wang@ozone.umsl.edu Message-ID: <3839C711.97ED2F7B@ozone.umsl.edu> Date: Mon, 22 Nov 1999 14:43:29 -0800 From: XIA WANG Organization: UMSL X-Mailer: Mozilla 4.7 [en] (X11; U; IRIX 6.2 IP22) X-Accept-Language: en To: CHEMISTRY@ccl.net Subject: How to convert a word file to PDF Dear ALL, I want to convert a word 97 file format to PDF format, please give me any suggestions or some covert software if necessory. Many Thanks, Wang, Xia begin:vcard n:; tel;fax:(314)516-5342 tel;home:(314)524-1178 tel;work:(314)516-6882 x-mozilla-html:FALSE org:Center for Molecular Electronics &;Department of Chemistry, UM-St.Louis adr:;;8001 Natural Bridge Road;St. Louis;MO;63121;USA version:2.1 email;internet:wang@ozone.umsl.edu title:Ph.D x-mozilla-cpt:;-18016 fn:Xia Wang end:vcard From chemistry-request@server.ccl.net Tue Nov 23 01:08:35 1999 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA20719 for ; Tue, 23 Nov 1999 01:08:35 -0500 Received: from voxopm.csc.fi (voxopm.csc.fi [128.214.248.23]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id HAA05146 for ; Tue, 23 Nov 1999 07:03:52 +0200 Date: Tue, 23 Nov 1999 07:03:51 +0200 From: Maija Lahtela To: chemistry@ccl.net Subject: How to freeze selected cartesian coordinates in Gaussian? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I would appreciate your help in my problem dealing with frozen cartesian coordinates with Gaussian 98. I have read the manual and tried in different ways without luck. The problem is that I would like to froze some of my carteesian coordinates and the rest of the coordinates should move freely. But how this should be done in my input-file ? Thanks in advance! Yours, Maija Lahtela-Kakkonen *************************************** Maija Lahtela-Kakkonen Researcher CSC-Center for Scientific Computing Tekniikantie 15 a D P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 FAX 358-9-4572302 E-MAIL mlahtela@csc.fi *************************************** From chemistry-request@server.ccl.net Mon Nov 22 18:18:24 1999 Received: from www.molecularmining.com (cgowave-16-35.cgocable.net [24.226.16.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA18979 for ; Mon, 22 Nov 1999 18:18:24 -0500 Received: from huxley (really [24.226.16.36]) by molecularmining.com via smail with smtp id (Debian Smail3.2.0.102) for ; Mon, 22 Nov 1999 16:52:39 -0500 (EST) From: "Ross M. Dickson" To: "CCL" Subject: Pharmacophore points Date: Mon, 22 Nov 1999 17:21:58 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Does anyone know of free or inexpensive software to compute pharmacophore points (e.g. H-bond donor, H-bond acceptor, +ve charge center, -ve charge center, lipophilic center, etc.) from a structure? I shall summarize if responses warrant. Thanks, Ross M. Dickson From chemistry-request@server.ccl.net Tue Nov 23 03:20:43 1999 Received: from biosci.cbs.umn.edu (eyoung@biosci.cbs.umn.edu [134.84.144.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA21642 for ; Tue, 23 Nov 1999 03:20:42 -0500 Received: from localhost (eyoung@localhost) by biosci.cbs.umn.edu (8.9.1/8.9.1) with SMTP id BAA01411; Tue, 23 Nov 1999 01:15:52 -0600 (CST) Date: Tue, 23 Nov 1999 01:15:52 -0600 (CST) From: Eva Young To: XIA WANG cc: CHEMISTRY@ccl.net Subject: Re: CCL:How to convert a word file to PDF In-Reply-To: <3839C711.97ED2F7B@ozone.umsl.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII adobe acrobat. www.adobe.com Eva Young University of Minnesota On Mon, 22 Nov 1999, XIA WANG wrote: > Dear ALL, > > I want to convert a word 97 file format to PDF format, please give me > any suggestions or some covert software if necessory. > > Many Thanks, > Wang, Xia > > begin:vcard > n:; > tel;fax:(314)516-5342 > tel;home:(314)524-1178 > tel;work:(314)516-6882 > x-mozilla-html:FALSE > org:Center for Molecular Electronics &;Department of Chemistry, UM-St.Louis > adr:;;8001 Natural Bridge Road;St. Louis;MO;63121;USA > version:2.1 > email;internet:wang@ozone.umsl.edu > title:Ph.D > x-mozilla-cpt:;-18016 > fn:Xia Wang > end:vcard > > > > -= 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 Tue Nov 23 03:41:10 1999 Received: from eros.campus1.ankara.edu.tr (eros.science.ankara.edu.tr [194.27.27.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA21751 for ; Tue, 23 Nov 1999 03:41:05 -0500 Received: from yfk1 ([212.50.47.137]) by eros.campus1.ankara.edu.tr (8.9.3/0.0.0) with SMTP id JAA12384; Tue, 23 Nov 1999 09:34:33 -0600 Message-ID: <000801bf3586$acd08620$892f32d4@yfk1.eros.science.ankara.edu.tr> From: "mehmet kabak" To: "XIA WANG" , Subject: Re: CCL:How to convert a word file to PDF Date: Tue, 23 Nov 1999 09:45:11 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-9" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Wang, you can use Acrobat Distiller to convert your Word97 to PDF. Mehmet Kabak >Dear ALL, > >I want to convert a word 97 file format to PDF format, please give me >any suggestions or some covert software if necessory. > >Many Thanks, >Wang, Xia > >begin:vcard >n:; >tel;fax:(314)516-5342 >tel;home:(314)524-1178 >tel;work:(314)516-6882 >x-mozilla-html:FALSE >org:Center for Molecular Electronics &;Department of Chemistry, UM-St.Louis >adr:;;8001 Natural Bridge Road;St. Louis;MO;63121;USA >version:2.1 >email;internet:wang@ozone.umsl.edu >title:Ph.D >x-mozilla-cpt:;-18016 >fn:Xia Wang >end:vcard > > > >-= 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 Tue Nov 23 07:00:41 1999 Received: from sg2.csrsrc.mi.cnr.it (sg2.csrsrc.mi.cnr.it [155.253.3.253]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA23465 for ; Tue, 23 Nov 1999 07:00:41 -0500 Received: from pit250.csrsrc.mi.cnr.it by sg2.csrsrc.mi.cnr.it via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id JAA01554; Tue, 23 Nov 1999 09:31:50 -0800 Message-Id: <3.0.1.16.19991123120212.2a3fddc4@sg2.csrsrc.mi.cnr.it> X-Sender: ale@sg2.csrsrc.mi.cnr.it X-Mailer: Windows Eudora Light Version 3.0.1 (16) Date: Tue, 23 Nov 1999 12:02:12 To: chemistry@ccl.net From: Alessandra Villa Subject: Complex solvation Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCL, I would like to solvate a complex by a predefinite water molecule using the the software Cerius2. Please, could explain me how I can build a complex solvated by water molecule. Thank you Best Regards Alessandra Villa ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Alessandra Villa PhD-Student Universita' degli Studi di Milano Dip. Chimica-Fisica ed Elettrochimica via Golgi 19 20133 Milano-Italy e-mail:a.villa@csrsrc.mi.cnr.it ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Tue Nov 23 07:54:24 1999 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA23764 for ; Tue, 23 Nov 1999 07:54:23 -0500 Received: from socrates-a.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (Mailer); Tue, 23 Nov 1999 11:49:29 +0000 From: uccatvm Message-Id: <4577.199911231149@socrates-a.ucl.ac.uk> Subject: Re: CCL:How to freeze selected cartesian coordinates in Gaussian? To: mlahtela@csc.fi (Maija Lahtela), chemistry@server.ccl.net (CCL) Date: Tue, 23 Nov 1999 11:49:33 +0000 (GMT) Cc: T.vanMourik@UCL.ac.uk (Tanja van Mourik) In-Reply-To: from "Maija Lahtela" at Nov 23, 99 07:03:51 am X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Maija, > I would appreciate your help in my problem dealing with frozen cartesian > coordinates with Gaussian 98. I have read the manual and tried in > different ways without luck. > > The problem is that I would like to froze some of my carteesian > coordinates and the rest of the coordinates should move freely. > But how this should be done in my input-file ? Did you have a look at the AddRedundant (or ModRedundant) option? It is not so difficult to use; just add "opt=AddRedundant" to the route section, and after the specification of the coordinates, list which ones you want frozen. For example, 1 2 F freezes the 1-2 distance 1 2 3 F freezes the 1-2-3 angle. Hope this helps, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Tue Nov 23 03:20:35 1999 Received: from uvaix7e1.comp.UVic.CA (root@uvaix7e1.comp.UVic.CA [142.104.5.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA21630 for ; Tue, 23 Nov 1999 03:20:34 -0500 Received: from p17-40.dialup.UVic.CA (p17-40.dialup.UVic.CA [142.104.17.40]) by uvaix7e1.comp.UVic.CA (8.9.3/8.9.3) with SMTP id XAA422134; Mon, 22 Nov 1999 23:15:44 -0800 From: royj@uvic.ca (Roy Jensen) To: XIA WANG Cc: chemistry@ccl.net Subject: Re: CCL:How to convert a word file to PDF Date: Tue, 23 Nov 1999 07:15:42 GMT Message-ID: <383b3d6e.1226187@pop.uvic.ca> References: <3839C711.97ED2F7B@ozone.umsl.edu> In-Reply-To: <3839C711.97ED2F7B@ozone.umsl.edu> X-Mailer: Forte Agent 1.5/32.451 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA21631 >I want to convert a word 97 file format to PDF format, please give me >any suggestions or some covert software if necessory. You need to purchase Adobe Acrobat (or find someone who owns it). Adobe is giving the Reader away for free but selling the software to create pdf files -- apparently very profitable given the abundance of pdf files available. The last time I checked, the price was 250$ US. Roy Jensen From chemistry-request@server.ccl.net Tue Nov 23 05:14:19 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 FAA22268 for ; Tue, 23 Nov 1999 05:14:18 -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 KAA00591; Tue, 23 Nov 1999 10:08:05 +0100 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: XIA WANG , CHEMISTRY@ccl.net Subject: Re: CCL:How to convert a word file to PDF Date: Tue, 23 Nov 1999 10:05:53 +0100 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <3839C711.97ED2F7B@ozone.umsl.edu> In-Reply-To: <3839C711.97ED2F7B@ozone.umsl.edu> MIME-Version: 1.0 Message-Id: <99112310080501.00563@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA22269 On Mon, 22 Nov 1999 XIA WANG wrote: >Dear ALL, > >I want to convert a word 97 file format to PDF format, please give me >any suggestions or some covert software if necessory. Since you use Word, I would suggest you _buy_ Acrobat Distiller to do the job. You also could print it to Postscript - using the free of charge Adobe Postscript printer driver, and convert that to PDF using the _free_ ghostscript. -- 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 Tue Nov 23 05:22:16 1999 Received: from uldns1.unil.ch (uldns1.unil.ch [130.223.8.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA22315 for ; Tue, 23 Nov 1999 05:22:15 -0500 Received: from pcbch3207h.unil.ch ([130.223.143.63] helo=pcbch3207h ident=aborel) by uldns1.unil.ch with esmtp (Exim 2.12 #1) id 11qC4m-0004iD-00; Tue, 23 Nov 1999 10:17:28 +0100 Message-ID: X-Mailer: XFMail 1.4.0 on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 In-Reply-To: Date: Tue, 23 Nov 1999 10:17:26 +0100 (MET) Organization: University of Lausanne Sender: aborel@pcbch3207h From: Alain Borel To: chemistry@ccl.net Subject: RE: CCL:How to convert a word file to PDF Cc: XIA WANG On 23-Nov-99 Eva Young wrote: > adobe acrobat. > > www.adobe.com > > Eva Young > University of Minnesota > > On Mon, 22 Nov 1999, XIA WANG wrote: > >> Dear ALL, >> >> I want to convert a word 97 file format to PDF format, please give me >> any suggestions or some covert software if necessory. You can also print to a PostScript file using the Windows PS printer driver and convert the file to PDF with Ghostscript (free, whereas Adobe distiller will cost $$$$). http://www.cs.wisc.edu/~ghost/  ---------------------------------- Alain Borel Year 2000: not the 21st century Date: 23-Nov-99 Time: 10:14:54 From chemistry-request@server.ccl.net Tue Nov 23 07:55:44 1999 Received: from raven.dcu.ie (raven.dcu.ie [136.206.1.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA23784 for ; Tue, 23 Nov 1999 07:55:42 -0500 From: Dermot.Brougham@dcu.ie Received: from ccmail-gw.dcu.ie by raven.dcu.ie (PMDF V5.1-10 #24113) with ESMTP id <01JIOC88XINC001T98@raven.dcu.ie> for chemistry@ccl.net; Tue, 23 Nov 1999 11:53:59 GMT Received: from ccmail.dcu.ie (ccmail.dcu.ie [136.206.5.1] (may be forged)) by ccmail-gw.dcu.ie (8.9.1a/8.9.1/893-FD) with SMTP id LAA25518 for ; Tue, 23 Nov 1999 11:46:23 +0000 (GMT) Received: from ccMail by ccmail.dcu.ie (ccMail Link to SMTP R6.00.02) id AA943350998; Tue, 23 Nov 1999 11:37:22 +0000 (GMT) Date: Tue, 23 Nov 1999 09:55:57 +0000 (GMT) Subject: PC or UNIX, G98 or Titan To: chemistry@ccl.net Message-id: <9911239433.AA943350998@ccmail.dcu.ie> MIME-version: 1.0 X-Mailer: ccMail Link to SMTP R6.00.02 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Dear CCler's, I have secured some (moderate) funding to get some hardware and software for QC calculations. I can now go one of several routes, though it is difficult to work out which is better (note there is a site licence here for G98 on UNIX). 1. A UNIX box running G98 2. A PC running G98 under LINUX 3. A PC running TITAN 4. A combnation of 2 & 3 My first question is which will run quicker given that I will be doing fairly large MP2 & B3LYP calculations and have the same sum to spend whatever route I go. My second question(s) (if I may) is about Titan: 1. Does it have a big library of basis sets and can you include basis sets from elsewhere in the input (eg for Ru)? 2. Is it recognised, i.e. would I have any trouble publishing results from it? 3. I am told the interface is good for both input and visualisation, is this generally accaepted? 4. I presume geometry optimization will work on cartesian coordinates and that it can transform to redundant internal coordinates. Can I input in z-matrix format too? Apologies for the length (and breadth) of the question; I will summarise the answers. Thanks Dermot Dr. Dermot Brougham School of Chemical Sciences Dublin City University Dublin 9 Ireland mail: dermot.brougham@dcu.ie From chemistry-request@server.ccl.net Tue Nov 23 11:41:35 1999 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA25352 for ; Tue, 23 Nov 1999 11:41:34 -0500 Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with SMTP id QAA09579 for ; Tue, 23 Nov 1999 16:36:44 +0100 (MET) Received: from pc03.chemie.uni-jena.de by pc04.chemie.uni-jena.de (5.65v3.2/1.1.10.5/28Jan98-0152PM) id AA22803; Tue, 23 Nov 1999 16:36:44 +0100 Sender: goeller@pc04.chemie.uni-jena.de Message-Id: <383AB48B.7DE1@pc04.chemie.uni-jena.de> Date: Tue, 23 Nov 1999 16:36:43 +0100 From: Andreas Goeller X-Mailer: Mozilla 3.04Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: chemistry@ccl.net Subject: SUMMARY: energy decomposition Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit 3 weeks ago I asked: #I'm looking for a method for intramolecular energy decomposition, #which is able to give the various contributions to the total energy #of rotational barriers like e.g. the ones in ethane, ethene ... # #The decomposition schemes of Morokuma and also of Ziegler seem to be #applicable only for intermolecular interactions, as is the version #available in Gamess. With NBO analysis I get Fock matrix energy terms #for various bond bond interactions, but here it seems that I am #restricted to one localized mesomeric structure. #I would like to have a consistent measure of steric, bonding and #antibonding, mesomeric contributions to total energy. #Is there any program available that can do this? I got 4 answers. Two of the people asked to summarize. The others suggested to following: 1) ADF: Tom Zieglers decomposition scheme publ. in Theor. Chim. Acta 2) Gamess: ________________________________________answers in details: Answer 1) Andreas Ehlers (answer in German) in short: with the mehod of Ziegler as implemented in ADF, it is possible to calculate - electrostatic interactions - Pauli repulsion (steric effects) - orbital interaction (occ. of one fragment with virt. of other) Answer 2) Jan Jensen Hello, GAMESS also offers the Localized Charge Distribution energy decomposition scheme. I have attached some references below. The early references use the original, semiempirical, implementation to look at rotation barriers in small molecules like ethane. The later papers use the method to study hydrogen bonding and proton transfer. Hope this helps. Best regards, Jan Jensen (a) W. England and M.S. Gordon, J. Amer. Chem. Soc. 93, 4649 (1971). (b) W. England and M.S. Gordon, J. Amer. Chem. Soc. 94, 4818 (1972 (c) M.S. Gordon and W. England, J. Amer. Chem. Soc. 94, 5168 (1972). (d) M.S. Gordon and W. England, Chem. Phys. Lett. 15, 59 (1972). (e) M.S. Gordon and W. England, J. Amer. Chem. Soc. 95, 1753 (1973). (f) M.S. Gordon, J. Mol. Struct. 23, 399 (1974). (g) W. England, M.S. Gordon and K. Ruedenberg, Theoret. Chim. Acta 37, 177 (1975). J.H. Jensen and M.S. Gordon "Ab Initio Localized Charge Distributions: Theory and a Detailed Analysis of the Water Dimer-Hydrogen Bond." J. Phys. Chem. 99, 8091-8101 (1995). Jan H. Jensen and Mark S. Gordon, "On the Number of Water Molecules Necessary to Stabilize the Glycine Zwitterion", Journal of the American Chemical Society, 1995, volume 117, pages 8159-8170. Mark S. Gordon and Jan H. Jensen, "Understanding the Hydrogen Bond Using Quantum Chemistry", Accounts of Chemical Research, 1996, volume 29, pages 536-543. 21. Ryan M. Minikis and Jan H. Jensen, "Towards a General Theory of Hydrogen Bonding: A Study of Hydrogen Bonds Involving H2O and HF", International Journal of Quantum Chemistry, in press. ____________________________________________________________ Additionally, I got some files with results regarding my chemical problem utilizing NBO 4.0 as implemented in Gaussian98, which has natural resonance theory and natural steric theory, but I'm not sure if these results fit to my problem... Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Nov 23 15:42:52 1999 Received: from arachne.eng.utah.edu (arachne.eng.utah.edu [155.99.222.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA26294 for ; Tue, 23 Nov 1999 15:42:52 -0500 Received: from lab3-20.eng.utah.edu (lab3-20.eng.utah.edu [155.99.222.219]) by arachne.eng.utah.edu (8.9.1a/8.9.1) with ESMTP id MAA21720 for ; Tue, 23 Nov 1999 12:37:59 -0700 (MST) Received: from localhost (montoya@localhost) by lab3-20.eng.utah.edu (8.9.3/8.9.3) with ESMTP id MAA24660 for ; Tue, 23 Nov 1999 12:37:58 -0700 (MST) X-Authentication-Warning: lab3-20.eng.utah.edu: montoya owned process doing -bs Date: Tue, 23 Nov 1999 12:37:58 -0700 (MST) From: Alejandro Montoya To: chemistry@ccl.net Subject: Ref. In-Reply-To: <383AB48B.7DE1@pc04.chemie.uni-jena.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to know where can I get the original papers of E. SchrOdinger equation in both, English and German if the version in English is available. It would be appreciated. Thanks in advance Montoya. From chemistry-request@server.ccl.net Tue Nov 23 17:29:47 1999 Received: from servidor.unam.mx (servidor.unam.mx [132.248.10.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA26764 for ; Tue, 23 Nov 1999 17:29:47 -0500 Received: from localhost by servidor.unam.mx (8.9.3/8.9.3) with SMTP id PAA18796; Tue, 23 Nov 1999 15:23:48 -0600 (CST) Date: Tue, 23 Nov 1999 15:23:48 -0600 (CST) From: "Alejandro Pisanty, DGSCA y FQ, UNAM" Reply-To: "Alejandro Pisanty, DGSCA y FQ, UNAM" To: Alejandro Montoya cc: chemistry@ccl.net Subject: Re: CCL:Ref. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Alejandro, the original 1926 papers are collected in a single volume called Wave Mechanics if my memory doesn't fail me too bad. You should also look at a very old book called "The Old Quantum Mechanics" by Ter Haar, and at Max Jammer's The Conceptual Development of Quantum Mechanics. I am not sure right now about the German version but they were published in Z. Phys., weren't they? Has someone reproduced this papers online? Alejandro Pisanty . . . . . . . . . . . . . . . . . . . . . . . . . . Dr. Alejandro Pisanty, Director General de Servicios de Computo Academico (Director, Computing Academic Services) Universidad Nacional Autonoma de Mexico (UNAM) Ciudad Universitaria, 04510 Mexico City DF MEXICO Tel. (+52-5) 622-8541, 622-8542; Fax 622-8540 . . . . . . . . . . . . . . . . . . . . . . . . . . From chemistry-request@server.ccl.net Tue Nov 23 17:58:39 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA26908 for ; Tue, 23 Nov 1999 17:58:38 -0500 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id NAA29122 for ; Tue, 23 Nov 1999 13:51:43 -0800 (PST) Received: from localhost (yadavm@localhost) by elvis.scripps.edu (8.9.2/TSRI-3.0) with SMTP id NAA318147 for ; Tue, 23 Nov 1999 13:51:43 -0800 (PST) Date: Tue, 23 Nov 1999 13:51:43 -0800 (PST) From: Maneesh Yadav To: chemistry@ccl.net Subject: InsightII remotely? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Anyone had any success in doing this? I am using ssh and other x apps seem to work fine, but insightII always gives me a NLS: 1 License(s) for Insight Checked Out loading internal data files Couldn't get initial visual in app_init_display I realize this will be unbearably slow, for the odd thing it can be very useful. Any ideas? I am running an intel linux box while the machine is an sgi octane, not that it should mattter (should it?). From chemistry-request@server.ccl.net Tue Nov 23 13:01:32 1999 Received: from ck-sg.p.lodz.pl (ck-sg.p.lodz.pl [212.51.207.68]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA25716 for ; Tue, 23 Nov 1999 13:01:25 -0500 Received: from piotr.p.lodz.pl (pc-212-51-214-182.p.lodz.pl [212.51.214.182]) by ck-sg.p.lodz.pl (8.9.3/8.9.3) with SMTP id RAA25013 for ; Tue, 23 Nov 1999 17:57:45 +0100 (MET) Message-ID: <029301bf35d3$7a361700$b6d633d4@p.lodz.pl> From: "Paneth" To: Subject: frequencies vs. coordinates Date: Tue, 23 Nov 1999 17:54:58 +0100 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0290_01BF35DB.DBB75B80" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 This is a multi-part message in MIME format. ------=_NextPart_000_0290_01BF35DB.DBB75B80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit > Dear all: > I have a question regarding frequency calculations in G98. Depending on > what's taken from the checkpoint, redundant internal or cartesian > coordinates the normal vibrations are somewhat different. Unfortunately, the > isotopic differences are so large that the isotope effects are not reliable. > Below I give an abbreviated version - full output files are attached. my original posting turned out to be too large for automatic distribution so the abovementioned files are zipped! > The question is which set should be trusted: > > 1st set: > ..... > #RHF 6-31++G** freq=(readisotopes,readfc) geom=check > ---------------------------------------------------- > 1/29=2,38=1/1; > 2//2; > 7/8=2,25=11/16; > 99/5=2/99; > ------------ > comment line > ------------ > No Z-matrix found on checkpoint file. > Cartesian coordinates read from the checkpoint file: > ....... > Frequencies -- 277.4024 357.4032 714.2104 > > 2nd set: > ..... > Redundant internal coordinates taken from checkpointfile: > ............ > Frequencies -- 278.9392 357.7119 701.2824 > --------- > Cheers, Piotr ****************************************************** Professor Piotr Paneth Department of Chemistry, Technical 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chemistry-request@server.ccl.net Tue Nov 23 18:58:00 1999 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA27326 for ; Tue, 23 Nov 1999 18:57:59 -0500 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay2.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id OAA19271 for ; Tue, 23 Nov 1999 14:51:03 -0800 (PST) Received: from localhost (yadavm@localhost) by elvis.scripps.edu (8.9.2/TSRI-3.0) with SMTP id OAA318226 for ; Tue, 23 Nov 1999 14:51:03 -0800 (PST) Date: Tue, 23 Nov 1999 14:51:03 -0800 (PST) From: Maneesh Yadav To: chemistry@ccl.net Subject: Re: InsightII remotely Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks to Joe Huang for letting me know that running insight like >insightII -axxess makes it use x graphics and allows it to run remotely. Just to let eveyone know, ssh is very nice and sets up display stuff for you, so there is no need to set the DISPLAY environment variable or xhost stuff.. Seems to be working for the most part. From chemistry-request@server.ccl.net Tue Nov 23 22:23:12 1999 Received: from jabez.anu.edu.au (jabez.anu.edu.au [150.203.193.248]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA28069 for ; Tue, 23 Nov 1999 22:23:10 -0500 Received: from localhost (really [127.0.0.1]) by jabez.anu.edu.au via in.smtpd with smtp (ident spg using rfc1413) id (Debian Smail3.2.0.102) for ; Wed, 24 Nov 1999 13:16:11 +1100 (EST) Date: Wed, 24 Nov 1999 13:16:05 +1100 (EST) From: Steve Greatbanks X-Sender: spg@jabez.anu.edu.au Reply-To: Steve Greatbanks To: CHEMISTRY@ccl.net cc: Maija Lahtela Subject: Re: CCL:How to freeze selected cartesian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Maija, > I would appreciate your help in my problem dealing with frozen cartesian > coordinates with Gaussian 98. I have read the manual and tried in > different ways without luck. > > The problem is that I would like to froze some of my carteesian > coordinates and the rest of the coordinates should move freely. > But how this should be done in my input-file ? There is a clear example given in the manual. The easiest way is to do something like the following. To freeze the cartesian coordinates of the oxygen whilst allowing the hydrogens to fully optimize; --start-- #p hf/3-21g opt=modredun nosym water constrained cartesian opt using opt=modredun 0,1 o 0.000000 0.000000 0.110334 h 0.000000 0.773410 -0.441334 h 0.000000 -0.773410 -0.441334 * B * F 2 A 3 A --stop-- Where * B builds a set of redundant internal coordinates based on cartesians and * F fixes all these redundants. 2 A and 3 A release the redundant internals related to the cartesians of h2 and h3. It is still perfectly feasible to use the old z-matrix optimiser and fix individual cartesian coordinates; viz --start-- #p hf/3-21g opt=z-matrix nosym water constrained cartesian opt using opt=z-matrix 0,1 o 0 0.000000 0.000000 0.110334 h 0 x1 y1 z1 h 0 x2 y2 z2 x1 0.000000 y1 0.773410 z1 -0.441334 x2 0.000000 y2 -0.773410 z2 -0.441334 --stop-- The redundant coordinate method is more flexible than the z-matrix optimizer in terms of the additional constraints which can be imposed, but the opt=z-matrix representation is pretty flexible. The use of nosym in the above jobs is deliberate and necessary if you wish to retain your input coordinate framework. Hope that is clearer, Steve Greatbanks -- +---------------------------------------+--+--------------------------------+ | Dr Stephen P. Greatbanks | | | | Biochemistry & Molecular Biology |w:| http://biocomp.anu.edu.au/~spg | | John Curtin School of Medical Research|e:| Steve.Greatbanks@anu.edu.au | | Australian National University |p:| (+61) (02) 6279 8305 (JCSMR) | | ACT 0200, Australia | | | +---------------------------------------+--+--------------------------------+ From chemistry-request@server.ccl.net Tue Nov 23 22:57:05 1999 Received: from iris.chem.cuhk.edu.hk (iris.chem.cuhk.edu.hk [137.189.38.205]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA28225 for ; Tue, 23 Nov 1999 22:57:04 -0500 Received: (from kurtz@localhost) by iris.chem.cuhk.edu.hk (8.9.3/8.9.3) id BAA02301; Thu, 25 Nov 1999 01:53:04 +0800 (HKT) Date: Wed, 24 Nov 1999 09:52:58 -0800 (PST) From: "Abe Kurtz W.L. Chiu" To: CHEMISTRY@ccl.net Subject: Scaling factor of B3LYP/6-31+G(d,p) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would like to know where I can get the reference about scaling factor of B3LYP/6-31+G(d,p). Thanks. Cheers, Kurtz W. L. A. Kurtz Chiu Dept. of Chem. CUHK E-mail :kurtz@iris.chem.cuhk.edu.hk Address: Department of Chemistry, Chinese University of Hong Kong Hong Kong