From chemistry-request@ccl.net Thu Jan 13 00:27:30 2005 Received: from smtp110.mail.sc5.yahoo.com (smtp110.mail.sc5.yahoo.com [66.163.170.8]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0D5RTg5005179 for ; Thu, 13 Jan 2005 00:27:29 -0500 Received: from unknown (HELO yahoo.com.cn) (yanliangren?2002@61.183.207.52 with plain) by smtp110.mail.sc5.yahoo.com with SMTP; 13 Jan 2005 05:27:27 -0000 Message-ID: <41E604EB.6080101$at$yahoo.com.cn> Date: Thu, 13 Jan 2005 13:19:39 +0800 From: yanliangren_2002 User-Agent: Mozilla/5.0 (X11; U; Linux i686; zh-CN; rv:1.2.1) Gecko/20030225 X-Accept-Language: zh-cn,zh MIME-Version: 1.0 To: chemistry$at$ccl.net Subject: How to get z-matrix coordination in chk file Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.1 required=7.5 tests=BAD_YAHOOMSGID, FROM_ENDS_IN_NUMS,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, everybody: How are u, I meet one problem, I want to read the z-matrix form geom coordination from .chk file when I do --Link1-- calculations, who can give me some advice? For instance, the first step I do opt for one molecular and then I want do freq calculations(I didn`t want to do OPT and FREQ by using together opt and freq) by --Link1-- keyword for which I must read the optmized in first step, and in this step I want to read the z-matrix form coordinates other than cartesian form from .chk file, and how we should to do? In addition to, I mainly intend to do it by setting in gaussian input file. Thanks best wish to u! From chemistry-request@ccl.net Wed Jan 12 19:57:42 2005 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0D0veg5024068 for ; Wed, 12 Jan 2005 19:57:41 -0500 Received: from chem.ucla.edu (d-128-97-138-237.chem.ucla.edu [128.97.138.237]) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id j0D0veRB003139; Wed, 12 Jan 2005 16:57:40 -0800 Date: Wed, 12 Jan 2005 17:03:15 -0800 Subject: Re: CCL:orbitals and reality Content-Type: text/plain; delsp=yes; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v553) Cc: chemistry^at^ccl.net To: Sengen Sun From: Eric Scerri In-Reply-To: <20050112053422.66343.qmail^at^web51304.mail.yahoo.com> Message-Id: Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.553) X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I havn't had a chance to look at the Nature paper in detail yet but I note on the first line of the paper that the authors say that orbitals are mathematical constructs or words to that effect. Why are they saying this since they promptly proceed to tell us that they have observed some orbitals? Now I need to read the paper and the editorial. Note also that no reference whatsoever is made to the reports from 1999 coming from Arizona State or any of the responses from those who disputed the claims. This is equally true of the primary paper and the editorial in Nature. regards, eric scerri On Tuesday, January 11, 2005, at 09:34 PM, Sengen Sun wrote: > Sorry for another posting on this subject. I am very > disappointed that I have not received any disagreement > to my earlier postings in the last two weeks. Instead, > I have been praised by four CCL friends who exchanged > personal e-mails with me. I wish to make a short > comment on one of Dr. Matt Challacombe's messages. > > I agree well with Matt. But the current problem is > much worse than one with a first year organic > chemistry student. It is about problems with some > scientific experts in the fields of physics and > chemical physcics. > > I just noticed that the Nature paper also made a front > page in C & En News (12/24/04) without mentioning the > controversies such as those mentioned in Dr. Eric > Scerri's JCE paper. A CCL friend used a quoted word > "triumph" to describe this situation and predicted > more "triumphs" are coming of orbital observation. > Unfortunately, these "triumphs" have already gone very > very wrong and gone way too too far. > > Why is that? Do we really care? > > Sengen > sengensun^at^yahoo.com > > > --- Matt Challacombe wrote: > >> I would say also that you can compute several of >> these >> properties without resorting to MO's at all, I >> believe. >> A coorespondence does not an existence proof make! >> (unless you are a first year organic chemistry major >> ;) >> >> -M >> > > > > > > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - now with 250MB free storage. Learn more. > http://info.mail.yahoo.com/mail_250 > > > -= This is automatically added to each message by the 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, jlabanow^at^nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095- 1569 E-mail scerri^at^chem.ucla.edu Tel: 310 206 7443 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@ccl.net Thu Jan 13 00:00:45 2005 Received: from mailhub1.uq.edu.au (mailhub1.uq.edu.au [130.102.148.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0D50hg5004136 for ; Thu, 13 Jan 2005 00:00:44 -0500 Received: from smtp2.uq.edu.au (smtp2.uq.edu.au [130.102.5.53]) by mailhub1.uq.edu.au (8.12.11/8.12.11) with ESMTP id j0D50gGI065180 for ; Thu, 13 Jan 2005 15:00:42 +1000 (EST) Received: from uq.edu.au (gonzo.soe.uq.edu.au [130.102.5.131]) by smtp2.uq.edu.au (8.12.10/8.12.10) with ESMTP id j0D50gJh002818 for ; Thu, 13 Jan 2005 15:00:42 +1000 (EST) Received: from [152.98.207.35] by msg2b.soe.uq.edu.au (mshttpd); Thu, 13 Jan 2005 15:00:42 +1000 From: Dr Seth OLSEN To: chemistry..at..ccl.net Message-ID: Date: Thu, 13 Jan 2005 15:00:42 +1000 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) MIME-Version: 1.0 Content-Language: en Subject: CCL: GAMESS/TINKER visualization of bulk model? X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 on UQ Mailhub X-Spam-Status: No, hits=4.5 required=7.5 tests=IMPRONONCABLE_1,TRACKER_ID autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi All, Does anyone on the list know of any software that can visualize the output of GAMESS/TINKER calculations (for example, optimizations) in such a way as to include the whole bulk model? It seems the ones I usually use only read in the quantum subsystem (i.e. the GAMESS results only). Just curious. Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Computational Systems Biology Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1..at..uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From chemistry-request@ccl.net Thu Jan 13 08:38:32 2005 Received: from vscan1-eur.ext.dsm.com (vscan1-eur.ext.dsm-group.com [163.175.162.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0DDcVvU028569 for ; Thu, 13 Jan 2005 08:38:32 -0500 Received: from vscan1-eur.ext.dsm.com (localhost [127.0.0.1]) by localhost.ext.dsm.com (Postfix) with ESMTP id 357CC7B7B for ; Thu, 13 Jan 2005 14:38:30 +0100 (MET) Received: from nlgln20ntms921.GLN20.DSM-GROUP.COM (nlgln20ntms921.gln20.dsm-group.com [172.20.36.51]) by vscan1-eur.ext.dsm.com (Postfix) with ESMTP id E4D8476E8 for ; Thu, 13 Jan 2005 14:38:29 +0100 (MET) Received: by nlgln20ntms921.gln20.dsm-group.com with Internet Mail Service (5.5.2657.72) id ; Thu, 13 Jan 2005 14:38:06 +0100 Message-ID: <6D47A7D05774D411959200508BDF739A044F0C08)at(nlgln50ntms001.gln51.dsm-group.com> From: "Coussens, Betty" To: chemistry)at(ccl.net Subject: refractive index computations Date: Thu, 13 Jan 2005 14:38:05 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: text/plain X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I am interested in computational methods that allow to predict the refractive index of a system (molecule or solid) as a function of wavelength. Is there anybody having experience with such type of computations? What methods can be employed and what about their accuracy? Thanks in advance! Sincerely, Betty This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately. From chemistry-request@ccl.net Thu Jan 13 04:37:37 2005 Received: from mta2.sucs.soton.ac.uk (mta2.sucs.soton.ac.uk [152.78.128.141]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0D9basE016557 for ; Thu, 13 Jan 2005 04:37:37 -0500 Received: from [152.78.196.193] (scarlet.chem.soton.ac.uk [152.78.196.193]) (authenticated bits=0) by mta2.sucs.soton.ac.uk (8.12.10/8.12.10) with ESMTP id j0D9b8ga008370 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NO) for ; Thu, 13 Jan 2005 09:37:08 GMT Message-ID: <41E6413F.1000106..at..soton.ac.uk> Date: Thu, 13 Jan 2005 09:37:03 +0000 From: Luca Fenu Reply-To: l.a.fenu..at..soton.ac.uk Organization: university of southampton User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7) Gecko/20040616 MultiZilla/1.6.4.0b X-Accept-Language: it, en-us, en MIME-Version: 1.0 To: chemistry..at..ccl.net Subject: assigning protonation states X-Enigmail-Version: 0.84.2.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-ISS-MailScanner: Believed to be clean X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CClers I'm looking for some program able to automatically (and reliably) assign protonation states at Phisiological pH to small organic molecules, preferably saved as mol2 files. As I can expect my boss ranting if he's to shed any money for it, any freeware alternative would be more than welcome. Any suggestion? many thanks luca -- Real programmers don't comment! It was hard to write, It should be hard to read! From chemistry-request@ccl.net Thu Jan 13 03:07:57 2005 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0D87msE011322 for ; Thu, 13 Jan 2005 03:07:53 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by smtp.unimi.it (8.12.11/8.12.11) with ESMTP id j0D86pjl017901 for ; Thu, 13 Jan 2005 09:06:54 +0100 (MET) (envelope-from alessandro.contini..at..unimi.it) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0IA800D9JX7E0U..at..smtp.unimi.it> for chemistry..at..ccl.net; Thu, 13 Jan 2005 09:06:50 +0100 (MET) Date: Thu, 13 Jan 2005 09:06:00 +0100 From: Alessandro Contini Subject: IRC with G03 In-reply-to: <20041209174625.55625.qmail..at..web50410.mail.yahoo.com> To: chemistry..at..ccl.net Reply-to: alessandro.contini..at..unimi.it Message-id: <200501130906.00816.alessandro.contini..at..unimi.it> Organization: =?iso-8859-1?q?Universit=E0=20di?= Milano MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 References: <20041209174625.55625.qmail..at..web50410.mail.yahoo.com> X-PMX-Version: 4.7.0.111621, Antispam-Engine: 2.0.2.0, Antispam-Data: 2005.1.10.49 X-PerlMx-Spam: Gauge=IIIIIII, Probability=7%, Report='__CD 0, __CT 0, __CTE 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __MIME_VERSION 0, __SANE_MSGID 0' X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j0D87vsE011329 Hi all, sorry for the late reply. I'd like to thank Joseph Han, Philip Hultin and Steve Williams for their replies. I perfectly agree with both Philip and Steve, it would be very useful to be able to force gaussian to recompute fc every a certain ammount of cycles. I followed your suggestion to calculate fc at each point and things went much better, however it took a really huge ammount of cpu time. Thanks again Alessandro -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini..at..unimi.it From chemistry-request@ccl.net Thu Jan 13 08:21:39 2005 Received: from smtp.bii-sg.org (nfs1000.bii.a-star.edu.sg [202.6.243.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0DDLbvU027701 for >ccl.net>; Thu, 13 Jan 2005 08:21:38 -0500 Received: (qmail 7657 invoked from network); 13 Jan 2005 13:21:32 -0000 Received: from unknown (HELO ?10.217.5.82?) (chandra@10.217.5.82) by apps5.bii.a-star.edu.sg with SMTP; 13 Jan 2005 13:21:32 -0000 Message-ID: <41E675D5.5000903<>bii.a-star.edu.sg> Date: Thu, 13 Jan 2005 21:21:25 +0800 From: Chandra >bii.a-star.edu.sg> User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL >ccl.net> Subject: EPR Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Can anyone kindly direct me to an idiot's introduction to EPR - with relevance to biology questions i am interested in getting an idea about relate to: what residues can be labelled easily and how how does distance between two sites affect the signal how does the space/medium between two sites affect the signal etc.... thanks very much chandra From chemistry-request@ccl.net Thu Jan 13 03:52:43 2005 Received: from web8409.mail.in.yahoo.com (web8409.mail.in.yahoo.com [202.43.219.157]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0D8qesE013175 for >ccl.net>; Thu, 13 Jan 2005 03:52:41 -0500 Received: (qmail 42421 invoked by uid 60001); 13 Jan 2005 08:52:39 -0000 Message-ID: <20050113085239.42419.qmail<>web8409.mail.in.yahoo.com> Received: from [202.141.117.38] by web8409.mail.in.yahoo.com via HTTP; Thu, 13 Jan 2005 08:52:39 GMT Date: Thu, 13 Jan 2005 08:52:39 +0000 (GMT) From: akila iyer >yahoo.co.in> Subject: CCL: problem with CIS optimisation To: CHEMISTRY<>ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello chemists, Good day.When I was trying to optimise a molecule(24 atoms) at CIS/6-31+g(d) level, the calculation stops after intial guess with the message as follows: "**** Warning!!: The largest alpha MO coefficient is 0.14478257D+03 Semi-Direct transformation. No file to extend for IUnit= 1 -- out of disk space. Error termination in NtrErr: NtrErr called from NtrExt. Can someone help me in this regard. Thank you with best regards Akila.L ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony