From chemistry-request@ccl.net Wed Jul 23 08:53:19 2003 Received: from linus.imcm.cas.cz (Linus.imcm.cas.cz [147.231.77.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6NCrIjq022520 for ; Wed, 23 Jul 2003 08:53:19 -0400 Received: from localhost (ccl@localhost) by linus.imcm.cas.cz (8.9.3/8.9.3) with ESMTP id OAA17302 for ; Wed, 23 Jul 2003 14:53:36 +0200 Date: Wed, 23 Jul 2003 14:53:36 +0200 (CEST) From: Petr Toman To: CHEMISTRY^at^ccl.net Subject: CCL: ZINDO + Si Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, does anybody know a reference for the ZINDO parameters of silicon? Thank you in advance. Regards, Petr Toman From chemistry-request@ccl.net Wed Jul 23 09:21:20 2003 Received: from webmail.mta.ca (rash.mta.ca [138.73.1.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6NDLKjq023548 for ; Wed, 23 Jul 2003 09:21:20 -0400 Received: from nobody by webmail.mta.ca with local (Exim 4.04) id 19fJYm-0000bE-00 for chemistry)at(ccl.net; Wed, 23 Jul 2003 10:21:36 -0300 Received: from 138.73.24.161 ( [138.73.24.161]) as user srwhttl)at(mailserv.mta.ca by webmail.mta.ca with HTTP; Wed, 23 Jul 2003 10:21:36 -0300 Message-ID: <1058966496.3f1e8be0cf1a8)at(webmail.mta.ca> Date: Wed, 23 Jul 2003 10:21:36 -0300 From: srwhttl)at(mta.ca To: chemistry)at(ccl.net Subject: MP2 Frequency Error MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.161 Hi, I got this error while trying to run a frequency calculation on uracil using mp2/6-31G*. Here is the printout at the end of the log file. Does anyone know what this message means? G2DrvN: will do 12 atoms at a time, making 1 passes doing MaxLOS=2. FoFDir used for L=0 through L=2. DD1Dir will call FoFDir 1 times, MxPair= 870 NAB= 435 NAA= 0 NBB= 0 NumPrc= 1. Petite list used in FoFDir. MinBra= 0 MaxBra= 0 Meth= 1. IRaf= 0 NMat= 870 IRICut= 1 DoRegI=T DoRafI=F ISym2E=-1 JSym2E=1. MaxTyp > LMax in AdjDF. Error termination via Lnk1e in /var/local/g98/l1112.exe. Job cpu time: 0 days 1 hours 44 minutes 6.6 seconds. File lengths (MBytes): RWF= 8855 Int= 0 D2E= 0 Chk= 4 Scr= 1 Thanks, Sarah Whittleton Mount Allison University From chemistry-request@ccl.net Wed Jul 23 08:38:54 2003 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 h6NCcsjq021756 for ; Wed, 23 Jul 2003 08:38:54 -0400 Received: from email.unb.ca (root-.at.-newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h6NCcokY003328 for ; Wed, 23 Jul 2003 09:38:50 -0300 Received: from [131.202.130.26] (HELO webmail1) by email.unb.ca (CommuniGate Pro SMTP 4.0.6) with ESMTP id 13830543 for chemistry-.at.-ccl.net; Wed, 23 Jul 2003 09:38:49 -0300 X-WebMail-UserID: s808o Date: Wed, 23 Jul 2003 09:38:45 -0300 Sender: Joey Harriman From: Joey Harriman To: CCL posting X-EXP32-SerialNo: 00003025, 00003442 Subject: termination link 9999 G98W Message-ID: <3F1F819E@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=0.8, required 5, SPAM_PHRASE_00_01) Hi, I am trying to do a qst2 calculation in Gaussian 98 to predict a transition state. However, at the end of the calculation I keep getting an error when the program is finalizing the calculation. The error says that the calculation has been terminated due to link 9999. Does anyone know how to resolve this problem. Any help would be greatly appreciated. Thanks in advance, Joey Harriman ---------------------------------- Joey Harriman MSc Computational Chemistry Toole Hall Room 228 Dept. of Chemistry University of New Brunswick Bag Service # 45222 E3B 6E2 454-1173 or 449-2543 ---------------------------------- From chemistry-request@ccl.net Tue Jul 22 17:31:05 2003 Received: from sentinel.ucr.edu (sentinel.ucr.edu [138.23.226.228]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6MLV4jq016807 for ; Tue, 22 Jul 2003 17:31:05 -0400 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentinel.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id ANV12371; Tue, 22 Jul 2003 14:31:02 -0700 (PDT) Reply-To: From: "Donald Keidel" To: Cc: Subject: CCL:Summary of pka database for carboxylic acids Date: Tue, 22 Jul 2003 14:31:00 -0700 Organization: UCR Message-ID: <000e01c35098$8ba62b40$529c178a@dopetec> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h6MLV5jq016808 Last message I sent I did not include the summary...duh. I want to thank everyone for their responses and suggestions. I ended up using ACD Labs prediction software and I am currently developing a binding affinity prediction equation with this information and other data. Sorry that the summary took so long to post, but I noticed today that I never did it and had all the e-mails marked as unread. Thank you again. Don SUMMARY: Hi Donald, if this is the case (you want to develop a computational prediction for your database) I suggest you then to use our software MIPSIM to preform a correlation between pka and molecular interaction potentials. It is free for download for academics and the opnly think you need is to have GAMESS (also free for academics) in your computer. You can also use GRID as your functuioin evaluator within MIPSIM, and I think it is also free for academics. Currently we are working to make the output compatible with GOLPE in order to get 3D-QSAR models from the dataset. I will tell Montserrat Barbany, who is actually touching the code, to put a snapshot for you in the web page when ready. The program can be found at Please, let me know if you have troubles downloading it. I hope this cover your needs. Jordi Hello Don, Per your question, check-out Pharma Algorithms, ADME Boxes software application www.admeboxes.com The evaluation software will give you 50 predictions for Ionization for free. Sounds like an interesting project. I'd be interested to hear how the software performed on your compound set. If you have further questions, contact me at your convenience. Regards, Paulius Jurgutis jurgutis-.at.-ap-algorithms.com Hi Donald, Once I was looking for a pka database with Google and I found this file, It may help you Regards Fabien Dear Don, The NIST provides a fairly comprhensive database for <$500. Alternatively, you might look for a copy of "Critical Stability Constants" by Martell and Smith in your local chemistry reading room. good luck- Steve Dear Mr. Keidel, Best database (not free) is shipped with ACDLab`s pKa estimation software. Best wishes, Andras Borosy If it's only carboxylates, an empirical method will probably do ok. If you don't want to splash out on a package, and only have 81 compounds, then you might like to try AcdLabs. It's not free but the cost is reasonable on a per-compound basis via web interface, and their database seems pretty substantial. They can also give references in case a compound has been measured. Otherwise... there was recently a substantial thread about this on the Accelrys QSAR mailing list... if you can't find the archive online I can try to dig up some of the posts. qsar_society-.at.-accelrys.com Hope this helps. Jeremy Hello Don, I guess you have already looked for the NIST critical stability constants? I found most of the logK-values I needed from there. In addition to the deprotonation values it contains also complexation constants with a variety of metal ions. Recently, the database has been available also in the web. It very likely requires a license though. Cheers, Atte ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec-.at.-dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm From chemistry-request@ccl.net Tue Jul 22 23:23:38 2003 Received: from smtp2.vtr.net (smtp2.vtr.net [200.83.1.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6N3NYjq028040 for ; Tue, 22 Jul 2003 23:23:36 -0400 Received: from smtp2.vtr.net (smtp2.vtr.net [200.83.1.20]) by smtp2.vtr.net (8.11.6/linuxconf) with ESMTP id h6N3NRX27026 for ; Tue, 22 Jul 2003 23:23:27 -0400 Message-ID: <001501c350c9$be985a10$52c453c8@xenon> Reply-To: "Diego Venegas-Yazigi" From: "Diego Venegas-Yazigi" To: "Computational Chemistry List" Subject: CCL: Atomic Orb. Coefficients in a Molecular Orbital analysis Date: Tue, 22 Jul 2003 23:22:53 -0400 Organization: Personal MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear CCLers I am interested in a Molecular Orbital composition analysis. I did Single Point calculations in Jaguar 4.2 and Gaussian 98 for Linux Rev A.9 and in both calculations the sum of the squared coefficients (atomic orbital coefficients) is not equal to 1, it is a different value for each MO. My question is how to normalise each MO to get a total sum (of the squared AO coefficients) equal to 1 (one). Thanks a lot to all Diego Venegas-Yazigi _________________________________________________ Dr. Diego Venegas Yazigi Postdoctoral Researcher New Magnetic Materials Laboratory Centre for the Advanced and Interdisciplinary Research in Material Science (CIMAT) Olivos 1007, Of. 313, Independencia, 8380492 Santiago, CHILE ----- W Ph. : 56 (2) 678-2801 Mobile : 56 (9) 841-8497 _________________________________________________ ---------------------------------------------------------------------------- ---- From chemistry-request@ccl.net Wed Jul 23 09:07:41 2003 Received: from webmail.mta.ca (rash.mta.ca [138.73.1.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6ND7fjq023044 for ; Wed, 23 Jul 2003 09:07:41 -0400 Received: from nobody by webmail.mta.ca with local (Exim 4.04) id 19fJLX-0000W0-00 for chemistry-.at.-ccl.net; Wed, 23 Jul 2003 10:07:55 -0300 Received: from 138.73.24.161 ( [138.73.24.161]) as user srwhttl-.at.-mailserv.mta.ca by webmail.mta.ca with HTTP; Wed, 23 Jul 2003 10:07:55 -0300 Message-ID: <1058965675.3f1e88ab1cdee-.at.-webmail.mta.ca> Date: Wed, 23 Jul 2003 10:07:55 -0300 From: srwhttl-.at.-mta.ca To: chemistry-.at.-ccl.net Subject: Gaussian Error MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.161 CCL, This error has came up with various calculations, all having to do with a DNA triplex BSSE calculation that has at least one base with ghosted atoms. It has also came up with someone else not working with DNA triplexes. I have tried adjusting the number of processors and also the memory being used, to no avail. I am running the calculations in parallel with Linda, over 8-16 processors. Here is the error message that comes up at the end of the file: "Warning! Spurious integrated density: NE= 136 NElCor= 0 Integral= 351.75570 Tolerance=1.00D-03 Consistency failure #2 in CalDSu. Error termination via Lnk1e in /usr/local/gaussian/g98/linda-exe/l502.exel." Thanks Sarah Whittleton Mount Allison University From chemistry-request@ccl.net Wed Jul 23 03:28:07 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 h6N7S7jq004996 for ; Wed, 23 Jul 2003 03:28:07 -0400 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Wed, 23 Jul 2003 08:28:06 +0100 Date: Wed, 23 Jul 2003 08:28:06 +0100 Message-ID: <3EFBE2180001614B=at=hawk.dcu.ie> From: noel.oboyle2=at=mail.dcu.ie Subject: Crystal structure vs geometry optimised structure To: 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 h6N7S7jq005000 Hello CCLers, I intend to carry out DFT calculations on inorganic complexes. In some cases I have crystal structures available. Is it better to use crystal structures as a starting point for energy and frequency calculations, or to use DFT-optimised structures? (where the DFT-optimised structure is in excellent agreement with the crystal structure) Thanks, Noel O'Boyle Han Vos Research Group, Dublin City University. From chemistry-request@ccl.net Wed Jul 23 15:38:59 2003 Received: from MM01SNLNTO.son.sandia.gov (mm01snlnto.sandia.gov [132.175.109.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6NJcxSK007206 for ; Wed, 23 Jul 2003 15:38:59 -0400 Received: from 132.175.109.1 by MM01SNLNTO.son.sandia.gov with ESMTP ( Tumbleweed MMS SMTP Relay 01 (MMS v5.5.0)); Wed, 23 Jul 2003 13:38:54 -0600 Received: from sandia.gov (s848769.sandia.gov [134.253.246.160]) by sass165.sandia.gov (8.12.9/8.12.9) with ESMTP id h6NJcoxI004354; Wed, 23 Jul 2003 13:38:51 -0600 (MDT) Date: Wed, 23 Jul 2003 13:38:43 -0600 Subject: Re: CCL:Atomic Orb. Coefficients in a Molecular Orbital analysis MIME-Version: 1.0 cc: chemistry=at=ccl.net To: "Diego Venegas-Yazigi" From: "Rick Muller" In-Reply-To: <001501c350c9$be985a10$52c453c8@xenon> Message-ID: <44A6EB3A-BD45-11D7-AB62-000A95823962=at=sandia.gov> X-Mailer: Apple Mail (2.552) X-PMX-Version: 4.0.1.70432 X-WSS-ID: 13003BC735778-01-01 Content-Type: text/plain; charset=us-ascii; delsp=yes; format=flowed Content-Transfer-Encoding: 7bit You need to multiply by the elements of the overlap matrix. For orbital index i and basis function indices a and b: 1 = Sum_ab c_ia*S_ab*c_ib R. On Tuesday, July 22, 2003, at 09:22 PM, Diego Venegas-Yazigi wrote: > Dear CCLers > I am interested in a Molecular Orbital composition analysis. I did > Single Point calculations in Jaguar 4.2 and Gaussian 98 for Linux Rev > A.9 > and in both calculations the sum of the squared coefficients (atomic > orbital > coefficients) is not equal to 1, it is a different value for each MO. > My > question is how to normalise each MO to get a total sum (of the > squared AO > coefficients) equal to 1 (one). > Thanks a lot to all > > Diego Venegas-Yazigi > > > _________________________________________________ > Dr. Diego Venegas Yazigi > Postdoctoral Researcher > New Magnetic Materials Laboratory > Centre for the Advanced and Interdisciplinary > Research in Material Science (CIMAT) > Olivos 1007, Of. 313, Independencia, 8380492 > Santiago, CHILE > ----- > W Ph. : 56 (2) 678-2801 > Mobile : 56 (9) 841-8497 > _________________________________________________ > > > > > > > > > ----------------------------------------------------------------------- > ----- > ---- > > > > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > > Rick Muller rmuller=at=sandia.gov From chemistry-request@ccl.net Wed Jul 23 16:45:03 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6NKj3SK008979 for ; Wed, 23 Jul 2003 16:45:03 -0400 Received: from dopey (dopey.ccmr.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3p2/8.9.3) with SMTP id QAA15394 for ; Wed, 23 Jul 2003 16:44:58 -0400 (EDT) Message-ID: <000801c3515b$487d4970$79f15480{at}ccmr.cornell.edu> From: "Connie Chang" To: Subject: CCL: Gaussian scripts? Date: Wed, 23 Jul 2003 16:44:59 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C35139.C15896A0" 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_0005_01C35139.C15896A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi -- I am running a multi-step job separated by the --Link1--- command. = Sometimes it gets stuck on a particular Force calculation and in those = cases, I'd like it to skip that job step and go on to the next one. Is = there a way to get Gaussian to do this? How? Thanks!=20 Connie ------=_NextPart_000_0005_01C35139.C15896A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi --
 
I am running a multi-step job separated = by the=20 --Link1--- command.  Sometimes it gets stuck on a particular Force=20 calculation and in those cases, I'd like it to skip that job step and go = on to=20 the next one.  Is there a way to get Gaussian to do this? =20 How?
 
Thanks!
 
Connie
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