From chemistry-request@ccl.net Tue Oct 26 00:43:47 2004 Received: from halifax.ks.uiuc.edu (halifax.ks.uiuc.edu [130.126.120.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9Q5hkll014522 for ; Tue, 26 Oct 2004 00:43:46 -0500 Received: from maputo.ks.uiuc.edu (maputo.ks.uiuc.edu [130.126.120.159]) by halifax.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id i9Q5uBxl024127 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Tue, 26 Oct 2004 00:56:19 -0500 (CDT) Date: Tue, 26 Oct 2004 00:56:08 -0500 (CDT) From: deyulu To: chemistry/at/ccl.net Subject: CCL:Gaussian Quadruple output question In-Reply-To: <5.2.1.1.0.20041007115435.034b58b0/at/pop.mater.unimib.it> Message-ID: References: <5.2.1.1.0.20041007115435.034b58b0/at/pop.mater.unimib.it> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed 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 have a question about Gaussian 03 Quadruple output. I have a neutral molecule carrying zero dipole. After a single point calculation, Gaussain outputs a Quadrupole moment and a Traceless Quadrupole moment. I used the input coordinates and Mulliken atomic charges to calculate the the Traceless Quadrupole moment, but they don't agree with the numbers in the output. Depending on the system, the two could be different by a factor of 2. Do you know whether Guassian uses Mulliken charges to calculate dipole and quadruple? What may cause such a difference? Thanks Deyu ************************************************************** Deyu Lu Tel: 217-367-7102(h), 217-244-8946(O) Office: 3111, Beckman Institute, UIUC Address: 2118 S. Orchard St., Apt. 203, Urbana, IL, 61801 ************************************************************** From chemistry-request@ccl.net Tue Oct 26 07:39:44 2004 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9QCdg5k001249 for ; Tue, 26 Oct 2004 07:39:43 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1CMQrD-00044V-25 for chemistry-.at.-server.ccl.net; Tue, 26 Oct 2004 09:55:23 -0300 Received: from 138.73.24.157 ( [138.73.24.157]) as user khunter-.at.-mailserv.mta.ca by webmail.mta.ca with HTTP; Tue, 26 Oct 2004 09:55:23 -0300 Message-ID: <1098795323.417e493b09813-.at.-webmail.mta.ca> Date: Tue, 26 Oct 2004 09:55:23 -0300 From: khunter-.at.-mta.ca To: chemistry-.at.-server.ccl.net Subject: CCL : request feedback about Lnk1e error MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.157 X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Single point calculation on cytosine dimer using the Basis Set of aug-cc-pvtz was performed using MP2 and the gen keyword for the basis set. A warning of : Warning: off-atom basis functions, so minimal bfn integration tests in XC quadrature. This warning was followed by: Spurious integrated density or basis function: NE= 58 NElCor= 0 El error=7.74D-06 rel=1.33D-07 Tolerance=1.00D-03 Shell 57 absolute error=9.54D-01 Tolerance=no limit Shell 85 signed error=4.79D-01 Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. Error termination via Lnk1e in /programs/g03/Rev_c02/g03/l401.exe Any advice as to the cause and solution to this error is greatly appreaciate. Ken Hunter Mount Allison University khunter-.at.-mta.ca From chemistry-request@ccl.net Tue Oct 26 08:43:32 2004 Received: from poincare.ciril.fr (medecine.uhp-nancy.fr [194.214.217.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9QDhV5k005027 for ; Tue, 26 Oct 2004 08:43:32 -0500 Received: from cbt.uhp-nancy.fr (host5.lctn.uhp-nancy.fr [193.50.239.5]) (authenticated bits=0) by poincare.ciril.fr (8.13.1/8.13.1/Guy-23-06-2004) with ESMTP id i9QDtaL1005897 (version=TLSv1/SSLv3 cipher=EXP1024-RC4-SHA bits=56 verify=NOT); Tue, 26 Oct 2004 15:55:36 +0200 (METDST) Sender: moreau_at_poincare.ciril.fr Message-ID: <417E5670.40909FFC_at_cbt.uhp-nancy.fr> Date: Tue, 26 Oct 2004 15:51:45 +0200 From: Yohann Moreau Organization: Equipe de Chimie et Biochimie =?iso-8859-1?Q?Th=E9oriques?= X-Mailer: Mozilla 4.7iC-CCK-MCD [en_US] (X11; I; AIX 4.3) X-Accept-Language: fr, en MIME-Version: 1.0 To: khunter_at_mta.ca CC: chemistry_at_server.ccl.net Subject: Re: CCL:CCL : request feedback about Lnk1e error References: <1098795323.417e493b09813_at_webmail.mta.ca> Content-Type: multipart/alternative; boundary="------------D2DA34DB4994027CA2BA66C5" X-Spam-Score: -2.323 () BAYES_00,HTML_MESSAGE,J_CHICKENPOX_31,J_CHICKENPOX_33,J_CHICKENPOX_54,J_CHICKENPOX_92,TW_BF X-Scanned-By: poincare.ciril.fr --------------D2DA34DB4994027CA2BA66C5 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, This error is, as far as I know, due to a failure in determining the guess wave function (in link 401). I've already had a similar problem with the Harris functional guess which is the default in G03. I'm not sure it is the solution, but you can try another method to determine the guess (typically INDO, the default in G98) by using the option : guess=indo (other are available, like EHT). Hope this helps, Yohann khunter_at_mta.ca wrote: > Single point calculation on cytosine dimer using the Basis Set of aug-cc-pvtz > was performed using MP2 and the gen keyword for the basis set. > > A warning of : > > Warning: off-atom basis functions, so minimal bfn integration tests in XC > quadrature. > > This warning was followed by: > > Spurious integrated density or basis function: > NE= 58 NElCor= 0 El error=7.74D-06 rel=1.33D-07 Tolerance=1.00D-03 > Shell 57 absolute error=9.54D-01 Tolerance=no limit > Shell 85 signed error=4.79D-01 Tolerance=1.00D-01 > Inaccurate quadrature in CalDSu. > Error termination via Lnk1e in /programs/g03/Rev_c02/g03/l401.exe > > Any advice as to the cause and solution to this error is greatly appreaciate. > > Ken Hunter > Mount Allison University > khunter_at_mta.ca > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Yohann MOREAU, Doctorant Equipe de Chimie et Biochimie Thioriques UMR CNRS-UHP 7565 "SRMSC" BP 239, F-54506 Vandoeuvre-lhs-Nancy http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html --------------D2DA34DB4994027CA2BA66C5 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello,

This  error is, as far as I know, due to a failure in determining the guess wave function (in link 401). I've already had a similar
problem with the Harris functional guess which is the default in G03.
I'm not sure it is the solution, but you can try another method to determine the guess (typically INDO, the default in G98)
by using the option : guess=indo  (other  are available, like EHT).

Hope this helps,

Yohann
 

khunter_at_mta.ca wrote:

Single point calculation on cytosine dimer using the Basis Set of aug-cc-pvtz
was performed using MP2 and the gen keyword for the basis set.

A warning of :

Warning:  off-atom basis functions, so minimal bfn integration tests in XC
quadrature.

This warning was followed by:

Spurious integrated density or basis function:
NE=   58 NElCor=    0 El error=7.74D-06 rel=1.33D-07 Tolerance=1.00D-03
 Shell    57     absolute error=9.54D-01              Tolerance=no limit
 Shell    85       signed error=4.79D-01              Tolerance=1.00D-01
 Inaccurate quadrature in CalDSu.
 Error termination via Lnk1e in /programs/g03/Rev_c02/g03/l401.exe

Any advice as to the cause and solution to this error is greatly appreaciate.

Ken Hunter
Mount Allison University
khunter_at_mta.ca

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-- 

               Yohann MOREAU, Doctorant                 
       Equipe de Chimie et Biochimie Théoriques   
               UMR CNRS-UHP 7565 "SRMSC"        
          BP 239, F-54506 Vandoeuvre-lès-Nancy  
http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html
  --------------D2DA34DB4994027CA2BA66C5-- From chemistry-request@ccl.net Mon Oct 25 17:29:46 2004 Received: from hotmail.com (bay10-f48.bay10.hotmail.com [64.4.37.48]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9PMTjll029473 for ; Mon, 25 Oct 2004 17:29:45 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 25 Oct 2004 15:42:11 -0700 Received: from 199.106.16.3 by by10fd.bay10.hotmail.msn.com with HTTP; Mon, 25 Oct 2004 22:41:06 GMT X-Originating-IP: [199.106.16.3] X-Originating-Email: [tomc1234/at/hotmail.com] X-Sender: tomc1234/at/hotmail.com From: "Tom Cao" To: chemistry/at/ccl.net Subject: Choice of Force field and charge Date: Mon, 25 Oct 2004 15:41:06 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 25 Oct 2004 22:42:11.0669 (UTC) FILETIME=[DDEA7850:01C4BAE3] X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS 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 have another question about the choice of force field or charge for the study systems. I found there are multiple choice of force fields when I want to make some calculations, could you please tell me some general rule, which force field is better for which system? (for example, marcomolecules, small molecules ...). What's about the choice of charges for different systems? Thanks a lot for your help Sincerely Tom _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ From chemistry-request@ccl.net Tue Oct 26 10:06:51 2004 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 i9QF6oG9009018 for ; Tue, 26 Oct 2004 10:06:50 -0500 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.11/8.12.11) with ESMTP id i9QFJNXE037814; Tue, 26 Oct 2004 18:19:24 +0300 (EEST) (envelope-from tamulis$at$mserv.itpa.lt) Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.12.11/8.12.11/Submit) with ESMTP id i9QFJNaj037811; Tue, 26 Oct 2004 18:19:23 +0300 (EEST) (envelope-from tamulis$at$mserv.itpa.lt) Date: Tue, 26 Oct 2004 18:19:23 +0300 (EEST) From: Arvydas Tamulis To: help$at$gaussian.com cc: CHEMISTRY$at$ccl.net, Jelena Tamuliene Subject: Optimization in transition state Message-ID: <20041026181205.Y34460$at$mserv.itpa.lt> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed 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 Colleagues, Would you please to help me because received unexpected stop during optimization in transition state of biological derivatives applying Gaussian03. The input line is follows: #P B3LYP 6-31G Opt=(TS,ModRedundant) IOp(6/3=12) DIIS SCFCYC=120 The optimization started, but after one cycle stopped: Optimization stopped. -- Wrong number of Negative eigenvalues: Desired= 1 Actual= 0 -- Flag reset to prevent archiving. My question is: what does it means these comments in G03 and how to avoid this stopping? Best regards, Arvydas Tamulis From chemistry-request@ccl.net Tue Oct 26 13:49:29 2004 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9QInSG9020157 for ; Tue, 26 Oct 2004 13:49:28 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.13.1/8.13.1) with ESMTP id i9QJ1gNK030042; Tue, 26 Oct 2004 16:01:42 -0300 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.11/8.12.8) with ESMTP id i9QJ1edg024205; Tue, 26 Oct 2004 16:01:40 -0300 Received: (from apache@localhost) by gollum.unb.ca (8.12.11/8.12.8/Submit) id i9QJ1en4024203; Tue, 26 Oct 2004 16:01:40 -0300 Received: from imac1.chem.unb.ca (imac1.chem.unb.ca [131.202.174.199]) by webmail.unb.ca (IMP) with HTTP for ; Tue, 26 Oct 2004 16:01:40 -0300 Message-ID: <1098817300.417e9f14b23dd^at^webmail.unb.ca> Date: Tue, 26 Oct 2004 16:01:40 -0300 From: Joe Harriman Reply-to: j.harriman^at^unb.ca To: Tom Cao Cc: chemistry^at^ccl.net Subject: Re: CCL:Choice of Force field and charge References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.174.199 X-UNB-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: X-MailScanner-From: s808o^at^unb.ca X-Spam-Status: No, hits=1.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR 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 Tom, With regards to your question concerning force fields and charge sets it is largely dependant on the size of the systems you wish to study. There are many varieties of forcefields available...each with it's own distinct advantages. Generally, the rule of thumb is that if you are studying small systems you can use a general force field (MMFF94, MM3, etc...). However, if you are studying large molecules (proteins for example) you would choose to use a specific forcefield (for example the Kollman series of forcefields for proteins that is implemented in AMBER). With respect to charge models, the best partial charges come from ab initio derived calculations. We have found that RESP charges are highly accurate. However, due to the nature of the high-level calculation these are not necessarily practical. You may want to look at models like AM1-BCC which require only a semi-empirical calculation followed by a charge correction. The advantage is that it is much faster and is somewhat similar to RESP charges. Finally, there are many other alternatives to calculate charges quickly like PEOE, mulliken, and Gasteiger methods. Hopefully this helps with your question. -Joe Harriman Quoting Tom Cao : > Dear All, > > I have another question about the choice of force field or charge for the > study systems. I found there are multiple choice of force fields when I want > to make some calculations, could you please tell me some general rule, which > force field is better for which system? (for example, marcomolecules, small > molecules ...). > > What's about the choice of charges for different systems? > > Thanks a lot for your help > > Sincerely > > Tom > > _________________________________________________________________ > FREE pop-up blocking with the new MSN Toolbar get it now! > http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Tue Oct 26 17:13:39 2004 Received: from mail.uvigo.es (mail.uvigo.es [193.146.32.69]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9QMDbG9030243 for ; Tue, 26 Oct 2004 17:13:38 -0500 Received: from [128.101.96.9] (rioja.chem.umn.edu [128.101.96.9]) (authenticated bits=0) by mail.uvigo.es (8.12.11/8.12.1) with ESMTP id i9QMQ6kW013759 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT); Wed, 27 Oct 2004 00:26:09 +0200 Subject: Re: CCL:Optimization in transition state From: Olalla Nieto Faza To: Arvydas Tamulis Cc: help.-at-.gaussian.com, CHEMISTRY.-at-.ccl.net, Jelena Tamuliene In-Reply-To: <20041026181205.Y34460.-at-.mserv.itpa.lt> References: <20041026181205.Y34460.-at-.mserv.itpa.lt> Content-Type: text/plain Organization: Universidade de Vigo Message-Id: <1098829565.11352.10.camel.-at-.rioja.chem.umn.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.6 (1.4.6-2) Date: Tue, 26 Oct 2004 17:26:05 -0500 Content-Transfer-Encoding: 7bit X-Virus-Scanned: "" 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 Just try to use "opt=(ts,noeigen, modredundant)" in your command line. What is happening is that the optimization algorithm checks the curvature of the hessian at each step, and tells the program to die if the number of negative eigenvalues is not the expected (one, in this case). When you use this keyword, the program will continue the optimization even if it finds no negative eigenvalue or more than one. In the gaussian manual (have a look at http://www.gaussian.com/g_ur/k_opt.htm ) they say it is not advisable to disregard this test, but I have been successfully using the "noeigen" keyword by default in my ts optimizations for quite a while (otherwise, unless you have very good initial guesses, you are often going to find this error message and see your calculations die in the first optimization steps). Regards, Olalla On Tue, 2004-10-26 at 10:19, Arvydas Tamulis wrote: > Dear Colleagues, > > Would you please to help me because received unexpected stop during > optimization in transition state of biological derivatives applying Gaussian03. > The input line is follows: > > #P B3LYP 6-31G Opt=(TS,ModRedundant) IOp(6/3=12) DIIS SCFCYC=120 > > The optimization started, but after one cycle stopped: > > Optimization stopped. > -- Wrong number of Negative eigenvalues: Desired= 1 Actual= 0 > -- Flag reset to prevent archiving. > > My question is: what does it means these comments in G03 and how to avoid > this stopping? > > Best regards, Arvydas Tamulis > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > -- ________________________________________________________________________________ Olalla Nieto Faza Ph: (+34) 986-813721 Graduate Student e-mail: faza.-at-.uvigo.es Dpto. Quimica Organica http://webs.uvigo.es/faza Universidade de Vigo Lagoas-Marcosende 36200 Vigo (Spain)